There is a FPS drop. I read the ISOs real slow with the CD Rom Drive and they're pretty much perfect (FF games work, so I think this is a problem with ISO caching).
I'm currently also testing using a Virtual Drive in combination with Pete's CDR plugin because it has a precache option which might help.
Another problem I'm having: Low FPS. Are some battles in Chrono Cross capped at 12 FPS or something? I can't figure out what's causing the slow down. Happens with the lowest settings in Pete's D3D and OpenGL2 plugins.