If your hotel is in Venice itself a taxi isn't going to help you once you get there. The only places that cars can go is Piazzale Roma or on the Lido island. To get around the city, you can walk, take a water taxi (very expensive), or take the vaporetto (water bus). There's a trip planner for the vaporetto here:
http://www.actv.it/english/home.php . There are night boats available, but obviously the schedule is somewhat reduced from the day time. You can also find schedules for land buses that circulate to the surrounding areas elsewhere on the site.
You won't have any trouble finding places where you can check in late. When you book the hotel, notify them of your expected arrival time. I've done the same thing on occassion and have never had any problem.