Dangerous Waters doesn't model nukes, sadly. I'm not too sure, but the RA/DWX mod might, never played it though.
Otherwise, you can "simulate" a nuclear launch, detonation, and/or impact through some clever scripting in the mission editor. Or go edit the database to make a weapon with one huge freaking explosion.
And as for the loss of Golf Class
K-129, well, that's certainly one theory. I think the official story is it sprung a leak of some sorts and fell below crush depth, which is entirely plausible considering all of the misfortunes the Soviets had with their boats. Though, after Project Arizona, I doubt anyone will ever know what happened to it for sure.