1.) None of those things may exist now.
2.) Why would you clutter up a reboot movie by making an unnessessary shopping list of references about the "defunct" timeline?
1). LOAF beat me to it, but some of them definitely SHOULD exist. The Doomsday machine, for example, would have been built and en-route to our galaxy long before the Kelvin was commissioned, or Kirk's father was even born, so it's hard to believe that Nero showing up would and destroying the Kelvin would have any effect on it having to be dealt with at some point. Likewise for V'ger, Nomad, etc. Sure some things might be different...with Kirk's brother following a different path, maybe the brain plague thing happens differently...but some things are still very much out there.
2). I wasn't suggesting that they should have put that stuff in the movie. I definitely wouldn't "clutter it up", as you say. I'm not even suggesting that they should show up in future movies. (Although if they do have any plans of using the reboooted movie as a launching point for yet another new TV series, I'm afraid all these issues give the writers very big handles to write episodes around instead of creatively coming up with new plots). I was just posing an interesting question.
Agree with LOAF that I would like to see a completely original story (if there is such a thing in Hollywood anymore), but that it would be fun to see a bunch of the iconic old TOS stuff get "burned off" acknowledging that maybe stuff like that did happen.