Nope. I believe it only removes the unused space on the rom.
Yes, it will work.
Although there are times when my ak2i won't play trimmed dsi games (always white screens), I think that was a bug with NDS Tokyo Trimmer. But it has the ability to skip dsi games, so no problem.
It is fixed.eh? I heard tokyotrim's author has fixed the dsi issue in new version... not yet?