Before, on a boat, I've seen big bars across the front doors which are secured by padlocks and then the usual lock.
I've also seen, how can I explain it.. the old "castle lock" type - Two side doors, each with a small but strong fixing position welded onto them, with a steel bar that can be put into place, this was on the stern doors, engine room doors and on the side door in the galley.
Most of the boat has portholes, which are secure due to their size, but the 3 windows on the boat have ornate bars, welded to either side of the window, which covers them which lets somebody break your windows which is a pain - but at least they can't get in, or get anything out!
One of my friends moored in Castlefields, which is basically Manchester city centre on the canal. They awoke one morning to find half of their stuff which they keep at the back end of the boat had gone. Obviously this is bad enough, but to find a lump hammer on the stern - The scum that broke in, obvously had this ready and waiting incase they woke up. I dread to think.