He only really missed alotof games in '10-'11. And this year...
His 5 year deal is up after next year, I think. They could work something out, but Orpik, Kunitz, and Letang are up at the same time, all three unrestricted. I'm guessing they'll let Kunitz go and focus on Malkin/Letang. Kunitz will be 34 and Orpik will be 33 and the rest of the core skaters are all mid-20's. It's not inconceivable that both older dudes will give the team a deal to stay and go for some Cups.
Probably comes down to whether Malkin wants to try leading his own team or not. He's a 2 time scoring champ and has shown he can carry a team when Crosby is hurt. If some team comes after him with wingers on par with what he's used to he could bolt. He's got a pretty cushy gig here and says he likes it, but he's Russian so it's not like he real forthcoming with his feelings. Crosby is locked up basically forever, barring catastrophic injury Malkin will never be THE MAN here. If he's fine with that and wants to stay they will make room, the front office is good at finagling the cap. And having 2 of the top 5 centers manning your top two lines is just way too huge an advantage to let go if you can help it.
Really too far out to speculate on money/cap hit though. They're projected 40mil under for that season right now, with like 5 guys signed=P