...tbh, that sounds more like a issue with how the game determines fleets more than anything. You'd think that more mods would equal more variety, but the game always ends favoring a few hulls per class.
That said, it does become pretty egregious when you pretty much only see one ship in a specific role. For Capitals, yep, Citadel. Cruisers... Huh, I can't actually recall running into any pirate cruisers so far. Destroyers seem to be almost entirely Kadur Falchions, with couple Takshido ships to prevent things from being completely red. Frigates have the closest thing resembling variety with three hulls being commonly used, though the Chimaera makes up the bulk.
I suppose the issue stands out a lot more when the ships the game settles on include some of the more annoying ones of the bunch.
Edit - Found a pirate fleet in waiting, here's what it looks like. Nice to see some cruisers in it at least, that class as a whole generally doesn't show up. All Hippogriffs though.
https://i.imgur.com/Qt8zf1f.jpgEdit 2 - I will agree with Marcoda on the Chimaera being awful to fight. They're not that much of a threat in terms of firepower, but their speed serves to pointlessly draw out a fight. They pretty much have all the annoyances that lead to phase ships getting their speed nerf, with no real novelty. Wouldn't be that bad if it was just a couple ships, but well... Swarms. Frankly, I had more fun losing ship to that group of Citadels than I did mopping up the Chimaeras.