This is very common occurance, Groo, I don' tknow how you haven't noticed it yet. No mods required.

Perhaps it's reasoned by my chosen map settings, yet.

Edit: ... and obiously by my lack of attention for this kind of details.

Good point, CaptainCobbs!

I reworked the weight table, perhaps it works now, using this file: WeightTableDefinitions.xml

I reworked this part (having only 30 names):

<GalaxyGeneratorWeightTable Name="SpecialNodeNames">
<Entry Tag="%SpecialNodeName1" Weight="1"/>
<Entry Tag="%SpecialNodeName2" Weight="1"/>
<Entry Tag="%SpecialNodeName3" Weight="1"/>
<Entry Tag="%SpecialNodeName4" Weight="1"/>
<Entry Tag="%SpecialNodeName5" Weight="1"/>
<Entry Tag="%SpecialNodeName6" Weight="1"/>
<Entry Tag="%SpecialNodeName7" Weight="1"/>
<Entry Tag="%SpecialNodeName8" Weight="1"/>
<Entry Tag="%SpecialNodeName9" Weight="1"/>
<Entry Tag="%SpecialNodeName10" Weight="1"/>
<Entry Tag="%SpecialNodeName11" Weight="1"/>
<Entry Tag="%SpecialNodeName12" Weight="1"/>
<Entry Tag="%SpecialNodeName13" Weight="1"/>
<Entry Tag="%SpecialNodeName14" Weight="1"/>
<Entry Tag="%SpecialNodeName15" Weight="1"/>
<Entry Tag="%SpecialNodeName16" Weight="1"/>
<Entry Tag="%SpecialNodeName17" Weight="1"/>
<Entry Tag="%SpecialNodeName18" Weight="1"/>
<Entry Tag="%SpecialNodeName19" Weight="1"/>
<Entry Tag="%SpecialNodeName20" Weight="1"/>
<!--<Entry Tag="%SpecialNodeName21" Weight="1"/>
<Entry Tag="%SpecialNodeName22" Weight="1"/>
<Entry Tag="%SpecialNodeName23" Weight="1"/>
<Entry Tag="%SpecialNodeName24" Weight="1"/>
<Entry Tag="%SpecialNodeName25" Weight="1"/>
<Entry Tag="%SpecialNodeName26" Weight="1"/>
<Entry Tag="%SpecialNodeName27" Weight="1"/>
<Entry Tag="%SpecialNodeName28" Weight="1"/>
<Entry Tag="%SpecialNodeName29" Weight="1"/>
<Entry Tag="%SpecialNodeName30" Weight="1"/>-->
</GalaxyGeneratorWeightTable>

Download the file and copy/paste it to this folder (by overwriting old file with same name) path: ...Steam/Steamapps/Common/Endless Space 2/Public/Galaxy Generator

Not sure so far, if you need to start a new game for testing, or if it should replace doubled node names immediately when loading "corrupted" save file. I hope it works, the one or the other way. If it doesn't, verify integrity of game files, to get back to official version (right mouse click on Endless Space 2 in Steam game list -> Properties -> Local files -> Verify integrity of game files). Feedback appreciated.

Edit: Past downloading file, rename it (from WeightTableDefinitions-1 to WeightTableDefinitions), as long as -1 is added to file name for whatever reason...