The more I think about it....

[failedALIAS]

No, Daniel lives in the ending where you knock over all the pillars. There must've been some way for him to have escaped, maybe the Shadow exploded all the walls of Brennenburg.

It's simple, the radiation from the orb and ''the shadow'' models being called spider eggs or whatever caused Daniel to become spiderman, which would provide an easy escape through the elevator shaft.

Okay, screw everyone else's theories; this is the one we should go with! It is the only one which covers ALL gaps present in similar observations. Either that, or another theory driven by Daniel's character model, which is nothing more than a hand and forearm. This theory states that Daniel IS Master Hand. He used his dimensional sorcery to conjure an escape.