Whenever I know I am checking in past midnight I always call the hotel (or email) and get confirmation that they know I am arriving late. In addition, I will usually utilize the online check-in function as well.

As aside: This system has always worked well for me but I typically do this when I am arriving off an international red-eye and want to ensure my room is ready upon arrival. I mention this because I've used it in cities where they are accustomed to people coming in really early.