I realize the best way to use CHDK is probably to have a separate memory card, but when I use my SD1100is, i prefer to travel light.
does the weight of an extra card make a difference ? :-)
On a more serious tone, having CHDK on your card won't make if slower.
Fragmentation is an issue when (for example) you shoot 1000 pictures and then you delete every second picture.... Doing this the free space on your card is all divided in pieces (fragmented) and write sepped might decrease.
if you really want to be sure, format the card, and then install chdk. this will ensure that all free spaces is in a single lump, after the chdk files.
I would say that rather than worrying about chdk files the thing you should reall avoid it to always selectively delete photos (in the long run, that's the largest cause for fragmentation), and sometimes delete all photos on your card, so that all the fragments are re-united in a llarge chunk.