To answer your question in the title of your post, no, lowering your IPD will not "affect" your frames per second.
Interpupilary distance adjustment should have no effect on FPS as it is only the measurement between the centre of one eye pupil and your other eye pupil and has no relevance to either your hardware ( electronics/rift gfx card etc ), similarly, if you adjust the seat in your car backwards or forwards it would not affect the performance of your car engine.
Hope this will help you.