Welcome!
I don’t have experience with the Nine 90, but I can tell you that in general, it’s cheaper to upgrade parts by buying a new bike. Just like you, I prefer to use things until they break, but the math just doesn’t work out when it comes to bikes. The bike companies get the parts really cheap, and they don’t mark them up as much as a retailer does.
I bet if you added up the retail value of all the parts on your $500 bike, you could easily get to $900. Also, while frames are big and obviously an integral part of the bike, hardtail frames aren’t all that valuable on their own. For example, you can buy an aluminum 29er frame from Nashbar for under $100:
http://www.nashbar.com/bikes/Product2_10053_10052_7000000000000003468_-1