First of all, changing the capital ship population cap is pretty easy, I've seen a few mods all changing it to different amounts. If you want to know how to do it, just ask, or if you really don't want to play around with it, then ask someone on the forums to make a quick pop cap mod. I've done it before for someone, only takes a few minutes or so.

As to the slow down, I don't know how much the cap is, but increasing the number of ships will takes it toll on the comp eventually, no matter what your PC specs are. The only difference is when you will experience the slow down.