I did stay in Venice for a week once. There are lots of bridges over the smaller canals it is true. However over the main canal where the shipping is they use the gondola taxis for people rather than a large bridge that would have to have a very high clearance.

When I was laying out my own Venice inspired city I routed all the ship traffic around the outside of the city and only have one bridge with that issue to block ships from entering that part of the city.

Plus with bridges it is much easier to charge a toll to cross, small boats just slip through the canals quietly to a secret meeting.