I support this Necro.
I like space pirates, that they are cliche makes them even more suitable to GalCiv. Space creatures would be cool too.
The way I would like to see pirates implemented would be as non playable Pseudo-Factions. Please not the boring Pirates from Endless space, those sucked.
I would like pirates you could interact with in many ways, You can negotiate with them, buy them off, trade with them, but all with the "reliability" you expect from pirates. They would appear kind of randomly, can colonize a planet here and there or make a Pirate Space station hidden somewhere that spawn ships. The techs they have would depend on what the other civs have, as all their techs are stolen. But maybe once in a while they can harvest an anomaly that gives them access to a better tech.
To be immersive they would need to actually be annoying to the main civs, or mildly helpful in some occasions. Wiping them out would result on some pirate free days but they could spawn out of nowhere again eventually. As they are off-shots from the main civs, a pirate group could be pf any race or a mix bag of them.
Pirates should start to appear sometime in late colony rush phase. Having them really early and hunting down your colony ships would be game breaking and not very fun, and not really believable for reasons op suggested.
And Also: Snathi Space pirates FTW!