Had that happen to me, too, and I am yet to find a secret door. Either it's the other crypts, like you say, or that particular one was generated in such a way that the poor Draugr was spawned in a hollow area obstructed by unbreakable walls. That same area might still be accessible in another crypt.
I think I even had it happen to me in burial chambers -- gentle jingly sound of bones but no skellies around anymore.