^Dumb question maybe, but at any point had you advised the hotel you were going to be arriving that late at night, and-or updated your ETA if you were delayed?
Some (many?) hotels have a policy that if you're not checked in by a certain time your reservation is cancelled and the room is open for walk-ins. I ran into this some years back - the hotel had a 10 p.m. check-in cutoff time, after which the reservation would be cancelled - prepaid in full, mind you, with no refund; due to a deal I'd got on it. My flight plus taxi wasn't going to get me there until 11 p.m. or so; I told the hotel this up front well in advance, they said no problem.
The plane didn't land until 2:30 a.m. local time (thanks, Air Canada!); by which time I'd called the hotel about five times with updates on my ETA. Again no problem, and a great week followed.
But had I not kept them advised, it's ironclad I'd have been out the reservation, the room, and a big whack o' cash. And stuck in a very full city looking for a hotel at 3 a.m.