are they going to ignore that he is alive in Valentine?

I'm fairly sure one of the DLC will be rescuing Valentine from being possessed by Kellog.

You'll have the option to kill, spare, or perhaps let Kellog takeover permanently.

I'm 90% sure.

That would be so awesome of a DLC, Kellogg possesses Nick and our favorite Synth detective becomes sort of a tragic villain as he wrestles with what is his own memories vs. the memories of Nick and Kellog's. Sadly, I doubt they'll do such a thing. :[

Well, it seems like a big set up in the main game.

Much like the Underwater City.

Also, the one empty cryopod in Vault 111.