Flashcarts don't affect the consoles, it's like if you were to take an empty DVD, put a movie on it and play it on your DVD player, the DVD player would play the movie but there wouldn't be any side effects. Same thing with flashcarts, you just put the games on them (or rather on the microSD card) and you can play them on the DS, but the DS itself won't change.
and one more thing
DS lite will not get update from Nintendo , so just buy a good flashcart with firmware support.