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 ...
The security folks aren't applying any judgement, they're just looking for things on a list of stuff that's not allowed. As long as big-ass servers aren't on the list and they fit in the carry-on size limit, it's all good.
I had a similar experience with lithium-ion batteries: I flew from Canada to the US with a backpack full of equipment that was 99% battery, 1% rfid reader by volume. On the x-ray, it looked like battery packs and that wouldn't have been allowed. But I told them it was rfid readers, and that made it okay.