From what I remember of my time with DCT, the gates had 2 every day uses.
1. To stop rubbish being drawn into the tunnel.Going down the weedhatch in the dark is no fun, and a boat can easily become wedged by a piece of floating timber in the tighter sections.
2. As you have correctly guessed, to stop boats getting in "out of hours".
Boaters have gotten stuck in "The Gaol" with the potential for personal injury, damage to the boat and tunnel, as well as creating chaos for the trip boats.
I dont think there is any conspiracy by BW or DCT to keep people out, its just that most boats dont fit.