As for why some wikis don't have adverts, I would imagine they are only monetised when the wiki reaches a sufficient level of activity/size. My test wiki is lacking adverts because of this.
Yes, but this announcement occupying a part of the mainpage. In other wikis I have this ad does not appear in the same place. This very disrupting the mainpage design. It's a shame! At least at main page I wanted a larger space for the layout.
See my wikis and the difference between them. An advertisement appears in no other.
Like I said, the adverts are obnoxious and non-negotiable. As a result, most wikis use main page column tags to work around the adverts.
I believe there was something going around about paying $20 to remove adverts from a wiki permanently, depending on how many page views your wiki had. This was a couple of years ago, so I'm not sure if it's still going.
If ads bother you this much, you'd be better switching to another network, such as http://www.wikkii.com, as their ads are at the top, not affecting your layout. If you'd like the features of Wikia, you can pay $20 per month or live with it. Talking to Wikia won't do anything.
This page has more information about it. Also, before giving Wikia money, remember this is only external ads: Adverts about Wikia (like spotlights and those annoying little site wide notifications) will still be present.