In mid-2001, notably before 9/11, I had to quickly move a 4U Sun Netra server from San Jose to Washington DC. I just carried it on. It was enormous - 4U and full length - and weighed a ton. No packaging, no box - just carrying a huge server down the aisle of the plane ...
I've flown with sketchy looking computers in pelican cases a few times. The only time it was a problem was when I mentioned that the batteries in the box were scooter batteries. Apparently you can fly with any size lead-acid batteries you want, but "scooter batteries" are on a list of specifically banned items. The security folks aren't applying any judgement, they're just looking for things on a list of stuff that's…
So far it's worked every time - not once have they asked if I could take them out; probably not so much that they're clueless as that they're just looking for the easiest way of getting their assigned task done.