Because from what I've seen it mainly affects your faction standings. Haven't gotten around to the sidequests yet but
do the sidequests affect your karma more so than MQ?

Your karma is more effected by your dialogue and your physical actions. IE, in one conversation, you are capable of telling an NPC to give you his clothes, or you'll kill him, this negates your karma. Doing good deeds and etc raise it.

once you get to liked or even accepted status. i have found that i have to steal ALOT of stuff to get a message about it and even then its only a "your a mischevious [censored]" that doesnt seem to have any game effect that i can see.