This happens every day. I've witnessed it myself: Going through transfer security (intl->domestic) at PHL, a (co)pilot was behind me at the x-ray. I made a comment about the lack of a special/priority crew lane there, and we had a chuckle that at least he got to keep his water bottle
I see two orthogonal ways to think about this:
(a) Since the TSA et al. are security theather anyway, the more exceptions the better. Why would you want your pilot to be dehydrated or pissed off?
(b) If the TSA et al. screening had any actual security value (i.e., not security theater), then the standard must be the same for everybody--the idea being to keep out certain items, regardless of who's holding them. Yes, a pilot can crash the plane with his hands, but a non-suicidal pilot can also hand off the explosives/guns/drugs/cash/whatevercontraband to somebody else inside the secure area, possibly without implicating themselves. Crew uniforms and badges can also be forged--another among many reasons why making exceptions based on someone's identity is problematic from a security perspective
Since (b) is so far fetched as to be laughable, I'll have to go with (a)...
Mentally ill pilots a la JetBlue are a whole different ballpark
