Gary Cahill apparently said to one of the reporters that he almost made it into today's squad and is confident of being fit for next week, and David Luiz seemed to be fit enough to run about like a madman after the Barca games and the FA Cup final, so it's very possible both could play.
Though even if they're both fit, neither have played a match for a long while, and I don't think Chelsea's record is that good when they've been the partnership at the back. Still, recently Chelsea's defending has started from the front and everybody has been helping eachother out, so any individuals missing isn't as big an issue as it might've been in the past / for other teams. They played 60 minutes at the Nou Camp with Bosingwa as a centre-half, for christ's sake!
Chelsea have defied the odds on numerous occasions in this season's competition and beating Bayern wouldn't really be their most surprising achievement, but there's no doubt who are the favourites (and still would be even if Terry, Ivanovic and Ramires were available). Even though they've been one of the most consistent performers in the competition for the last decade, and would probably rank 2nd or 3rd on the UEFA coefficients, if Chelsea can win it they'll be the most surprising victors since Porto... or perhaps moreso in hindsight, when you consider what those Porto players and manager have proven since.
Di Matteo deserves the job whatever happens.