As long as things stay conventional, they and other assets will be useful. But in an escalating nuclear conflict, you're right, they'll probably be goners, along with a lot of other stuff. That is the conundrum we face. We need both a credible nuclear deterrent and a strong conventional component. That takes money and my sense is that Bro and his boys aren't going to fund it. They have "other priorities" (i.e., welfare and lining up for "Obama Money").
Sooner or later (preferably sooner), the Nav is going to have to look at countering the threat the AIP subs pose to carrier groups. I know their range and time on (submerged) station is limited, but they add another dimension to quietness.
I bet the carriers would last longer than a Bomber base or missile sight.