Usually it is mentioned, when it is not, it is usually something that needs to be done, that you take it upon yourself to do for the good of your faction. If you choose not to whatever.
I kinda like them. I mean, encouraging a little extra grinding is a good thing. This way people are less likely to end up in an area underlevelled. If they did as you suggest and just raised mob XP and did away with bonus quests, this would encourage straight grinding and people skipping more of the story and side quests. I understand some people skip them all anyway, but some people enjoy them, if there was no reason to do them or there was really no reason other than the story to do it, then what is the point in having it there? Seeing as they spent money getting it in they wanted to encourage people to do it.