ASP.Net forums will get indexed in exactly the same way as PHP forums. As far as search engines are concerned it's just another webpage, doesn't really matter how it got generated.
With regards to your choice of package, if you're really after an ASP.Net board, have a look at CommunityServer (
http://communityserver.org/) which is one of the better ASP.Net ones.
You will find however that there's more choice in the PHP space, as well as more mods, supports and templates for PHP boards. If the decision was mine (even though I'm firmly in the Microsoft space in my day job), I would prefer to go down the PHP route.
Hope this helps
Owen