<p>I am using MSBuild to build my stuff. I want to use CruiseControl.net as by Build Server.</p>

<p>Now, CCNET refers nAnt a lot, but it looks as if ccnet can do most of the stuff nant could do through the project configuration and msbuild. Also, nAnt seems a bit unsupported, with a Beta release that is almost a year old now.</p>

<p>In short: I am actually quite happy with MSBuild (especially since it's the "official" compiler front end) and a bit uncomfortable with nAnt, but I do not want to judge prematurely.</p>

<p>What would be reasons to use nAnt over MSBuild? Especially with ccnet, which seems to overlap a bit with nant in terms of features (and adding the automated build related stuff)</p>

In my opinion it is more a question of personal preference.  nAnt is a great framework and MSBuild is almost as capable.  With the ability to easily develop custom tasks (in both frameworks) you can accomplish almost anything that you need to do.
I cannot answer the "still supported" portion of your questions, but I would say if you are already comfortable with nAnt then it's probably viable.  If you (or someone in your group) is familiar with MSBuild then that is a fine way to go as well.