I'm a little confused. As I understand it, is it that each minor faction has a single visually unique ship that corresponds with a particular class of ship? Or are they going to share a visual between ideology (i.e. all Science focused minor factions have the same visual style) Based off the of the videos thus far, the art style being used by all of the minor faction ships seem to belong most to the Epistis...

All these ships will have different uses, however, thanks to modules and hulls having different availability even within a same family. 

Speaking of ship modules, why did the Sophon ships have open gun ports? Can certain hull variations only hold so many guns/other modules?

That strikes me as a very reasonable assumption.

No, the Deuyivans will have a different ship family.

That is correct, there will be 4 "families" which correspond to looks. This is a production constraint, as having 2-3 ships per faction for 16 minor factions would mean essentially as much work as another 6 sets of major factions, which we simply couldn't afford. 

All these ships will have different uses, however, thanks to modules and hulls having different availability even within a same family.

If i remember correctly minor factions will have 4 ships' "families"