Yeah, the engine actually handles high polycounts quite well. Texture rendering and computing shield collisions (though Bobboau has some ideas on improving that one... by orders of magnitude, from what I hear) are bigger performance issue.
And the thing about polycounts is that as long as the LODs are well done, people can lower them on the fly using the model detail slider in options - Which doesn't actually reduce model detail up close, it just makes lower LODs kick in earlier, so you still get all the details when you're skimming the hull of a Star Destroyer or ramming a poor unshielded TIE. So basically, model for high-end systems, and people with low-end systems can adjust their settings to match and all will be well, as the detail options are there for a reason.
Also, there are a few things that can be done to cut on-screen polycounts without actually changing the models. You probably know about them already but I'll mention it anyway on the off chance you don't: In ships.tbl, the "POF target file" and "POF target LOD" options can be used to specify which model and LOD are used for the target box model, which can potentially cut several thousand on-screen polys when a very detailed ship is targeted. And for larger ships, detail boxing can do wonders for areas that need particularly intricate modelling, essentially working as a kind of local LOD.
