In Batman Begins, the implication is that Bruce (and Alfred) used the construction of an additional set of foundations as a ruse to improve his underground base:
Bruce Wayne: Rebuild it. Just the way it was, brick for brick.
Alfred Pennyworth: Just the way it was, sir?
Bruce Wayne: Yeah. Why?
Alfred Pennyworth: I thought this might be a good opportunity for improving the foundations.
Bruce Wayne: In the south-east corner?
Alfred Pennyworth: Precisely, sir.
Given the layout of the Batcave I see no good reason to assume that the contractors would have thought that they were building anything other than an oversized underground parking garage for Bruce Wayne, the notably eccentric billionaire and sport-car enthusiast. I'm guessing they were also made to sign really restrictive non-disclosure agreements.