If they don't collect your cert and Hilton picked up the tab for the hotel I'd have to say I'd be happy with that. If they still want the cert I'd probably ask for some "points" as compensation for your troubles. Although I've not had many problems with hiltons, the upgrade to a suite at 12:45 am while nice isn't really that great of a perk cuz I'm only gonna enjoy seeing the inside of my eyelids and I could just as well be in any room doing that.
But if I was keeping the points and they paid for the room I would write a letter saying it could have been more proactively handled and ready to go once you got there but that they worked diligiently and did a good job of taking care of you while you were waiting.
Lance