Maybe this is because the quote "Any sufficiently advanced technology is indistinguishable from magic." would imply that the computer would stop working ? (This was only intended as a pun, as the reason is most likely the author prefers the other set of characters, but having the kernel panic handling module be named Touma would add to the spirit)

For those that would (most understandably) not get the reference in those names, there is a novel saga called "To Aru Majutsu no Index"/"a certain magical index", which the name references (to aru == "a certain"), and Misaka/Kuroko are characters from it.

By the way, is Yutani a reference to something ?

Fukou da.