Short answer, yes, this can be done.  I went ahead and created a Vodyani Hero Ship mod. 

You'd likely have to create a mod for each faction, as the ship defintions are unique and you wouldn't be able to have multiple definitions for the same named Hull. 

For example, in the HullDefinitions.xml file, there is a definition defined as "Hull01SmallAdventurer".  Let's say I wanted to replace the ship with the Vodyani Medium Attacker ("HullMedium01Vampirilis").

Actually, I just went ahead and did it. Here's a couple of screenshots of the result:

Main screen:

Going the TLDR; route...here is the modified hull definition I used to create the above:

    <HullDefinition Name="Hull01SmallAdmiral">

        <PathPrerequisite Flags="Prerequisite,Discard,Faction">./ClassEmpire/ClassPopulationEmpireAffinityVampirilis,PopulationMajor</PathPrerequisite>
        <PathPrerequisite Flags="Edition,Faction">ClassEmpire/ClassPopulationEmpireAffinityVampirilis,PopulationMajor</PathPrerequisite>

        <SimulationDescriptorReference Name="ClassHullMediumAttack"/>
        <SimulationDescriptorReference Name="WeaponAvailabilityKinetic"/>
        <SimulationDescriptorReference Name="WeaponAvailabilityBeam"/>
        <SimulationDescriptorReference Name="WeaponAvailabilityLaser"/>
        <SimulationDescriptorReference Name="WeaponAvailabilityMissile"/>
        <SimulationDescriptorReference Name="ShipSizeMedium"/>
        <SimulationDescriptorReference Name="ShipFactionVampirilis"/>
        <SimulationDescriptorReference Name="ShipHull01"/>

      <ShipDesignLayout>
            <ShipRoleReference Name="ShipRoleMediumAttacker"/>
            <SectionPattern_Eight>
                <!-- Core Section -->
                <CoreSection Name="CoreSection">
                    <VisualSectionName>Core</VisualSectionName>
                    <SimulationDescriptorReference Name="ClassSectionCore"/>
                    <SimulationDescriptorReference Name="ClassSectionCoreMediumOffense"/>
                    <Slot Name="Support01">
                        <RestrictedModuleCategory>Support</RestrictedModuleCategory>
                        <Direction X="0" Z="1"/>
                        <ModuleModifier>
                            <SimulationDescriptorReference Name="MultiplierX2"/>
                        </ModuleModifier>
                        <UISlotName>UICore09</UISlotName>
                    </Slot>
                    <Slot Name="Defense01">
                        <Cost ResourceName="Strategic3" Instant="true">1</Cost>
                        <TechnologyPrerequisite Flags="Prerequisite,Discard">TechnologyImproveHull3</TechnologyPrerequisite>
                        <RestrictedModuleCategory>Defense</RestrictedModuleCategory>
                        <Direction X="0" Z="1"/>
                        <ModuleModifier>
                            <SimulationDescriptorReference Name="MultiplierX2"/>
                        </ModuleModifier>
                        <UISlotName>UICore10</UISlotName>
                    </Slot>
                    <Slot Name="Weapon01" ShowPositionMarker="true" PositionMarkerAngle="0">
                        <RestrictedModuleCategory>Weapon</RestrictedModuleCategory>
                        <RestrictedModuleCategory>Support</RestrictedModuleCategory>
                        <LineOfSight>
                            <Direction X="0" Z="1"/>
                            <Angle>270</Angle>
                            <VisualSlotName>MDL_Wp_Small_Up_02</VisualSlotName>
                            <VisualSlotName>MDL_Wp_Small_Up_03</VisualSlotName>
                        </LineOfSight>
                        <ModuleModifier>
                            <SimulationDescriptorReference Name="TopWeapon"/>
                            <SimulationDescriptorReference Name="MultiplierX2"/>
                        </ModuleModifier>
                        <UISlotName>UICoreWeapon11</UISlotName>
                    </Slot>
                    <WeaponSlot Name="LargeWeapon01" IsLargeSlot="true" ShowPositionMarker="true" PositionMarkerAngle="135" ModuleCostMultiplier="2">
                        <Cost ResourceName="Strategic3" Instant="true">2</Cost>
                        <TechnologyPrerequisite Flags="Prerequisite,Discard">TechnologyImproveHull3</TechnologyPrerequisite>
                        <LineOfSight>
                            <Direction X="0" Z="1"/>
                            <Angle>270</Angle>
                            <VisualSlotName>MDL_Wp_Medium_Up_00</VisualSlotName>
                        </LineOfSight>
                        <ModuleModifier>
                            <SimulationDescriptorReference Name="TopWeapon"/>
                            <SimulationDescriptorReference Name="LargeWeapon"/>
                            <SimulationDescriptorReference Name="MultiplierX2"/>
                        </ModuleModifier>
                        <UISlotName>UICoreWeapon12</UISlotName>
                    </WeaponSlot>
                </CoreSection>

                <!-- Forward Section -->
                <Section Name="SectionN">
                    <VisualSectionName>Front</VisualSectionName>
                    <Slot Name="Defense01">
                        <RestrictedModuleCategory>Defense</RestrictedModuleCategory>
                        <Direction X="0" Z="1"/>
                        <ModuleModifier>
                            <SimulationDescriptorReference Name="MultiplierX2"/>
                        </ModuleModifier>
                        <UISlotName>UIFront01</UISlotName>
                    </Slot>
                    <Slot Name="Weapon01" ShowPositionMarker="true" PositionMarkerAngle="30">
                        <Cost ResourceName="Strategic3" Instant="true">1</Cost>
                        <TechnologyPrerequisite Flags="Prerequisite,Discard">TechnologyImproveHull3</TechnologyPrerequisite>
                        <LineOfSight>
                            <Direction X="0" Z="1"/>
                            <Angle>270</Angle>
                            <VisualSlotName>MDL_Wp_Small_Up_00</VisualSlotName>
                            <VisualSlotName>MDL_Wp_Small_Up_01</VisualSlotName>
                        </LineOfSight>
                        <ModuleModifier>
                            <SimulationDescriptorReference Name="TopWeapon"/>
                            <SimulationDescriptorReference Name="MultiplierX2"/>
                        </ModuleModifier>
                        <UISlotName>UIFrontWeapon02</UISlotName>
                    </Slot>
                </Section>

                <!-- Forward/Right Section -->
                <Section Name="SectionNE">
                    <VisualSectionName>FrontRight</VisualSectionName>
                    <Slot Name="Defense01">
                        <RestrictedModuleCategory>Defense</RestrictedModuleCategory>
                        <Direction X="1" Z="0"/>
                        <ModuleModifier>
                            <SimulationDescriptorReference Name="MultiplierX2"/>
                        </ModuleModifier>
                        <UISlotName>UIFrontRight03</UISlotName>
                    </Slot>
                </Section>

                <!-- Right Section -->
                <Section Name="SectionE">
                    <VisualSectionName>Right</VisualSectionName>
                    <Slot Name="Defense01">
                        <RestrictedModuleCategory>Defense</RestrictedModuleCategory>
                        <Direction X="1" Z="0"/>
                      &nb

Wow. Thank you, Knightefall, I'll go ahead and try to do this for other factions as well.

EDIT : I found these lines in the HeroDefinition.xml document : 

    <!-- VAMPIRILIS -->
    <HeroDefinition Name="HeroVampirilis01">
        <Skill Name="HeroSkill01Vampirilis01"/>
        <Skill Name="HeroSkill02Vampirilis01"/>

        <Affinity Name="HeroAffinityVampirilis"/>
        <Class Name="HeroClassAdmiral"/>
        <Politics Name="HeroPolitics04"/>

        <ShipDesign Name="ShipDesignHeroSmall01Attacker"/>

        <SkillTree Name="HeroSkillTreeGeneric"/>
        <SkillTree Name="HeroSkillTreeVampirilis"/>
        <SkillTree Name="HeroSkillTreeAdmiral"/>
        <LevelUpRuleReference Name="HeroLevelUpRule"/>
    </HeroDefinition>

Wouldn't it be a "lazy" way to change the Hero ships, by editing  <ShipDesign Name="ShipDesignHeroSmall01Attacker"/> ? 

I say "lazy" cause it would probably just replace the ship with a standard one, when Heroes shups have usually more abilities, like they can carry probes.

Or am I completely wrong ?