No, no, it won't affect game speed or input lag at all. Only page load time, and I think even that hit won't be too bad, perhaps not even noticeable. On another note, I've noticed some browsers are not too efficient rendering the current page layout. Chromium and Firefox seem to do just fine, but for example Midori scrolls the game area a bit slowly. Not unplayable on it either, though.
Yes, it would be possible to decrease saturation. Just do a RGB->HSV transformation to the pixels, tune saturation, then convert back to RGB. Easy as pie.
Anyway, I've set this effect for version 1.1. The most important thing now is to get the game to a state where I can start beta tests, in other words when 1.0 is feature-complete. First things first.