You are correct that the Netduino Go is a bit older (originally released in 2012) and the Netduino 3 is the most recent Netduino (released only a few weeks ago). I covered a bit of the Netduino Go's history in my blog post/review here.
Chris will probably be able to tell you more about the Netduino Go's future, but my understanding is that it's only temporarily missing from the main product lineup page. It's still receiving firmware updates, support, etc. at this point.
If you're only using Go modules, need more than 3 GoBus ports, and don't need Wi-Fi or Ethernet, the Go mainboard is still a good choice. Otherwise, I'd choose the Netduino 3

Matt