There is no limit to the number of zones you can maintain in the fleet management application. If anything, a large number of zones may impact performance.
What impacts performance:
Shape of zones: quadrants are ideal, "circles" are not.
Default property: Indicate stops within zone. If this is on there is a system rule that breaks whenever a vehicle stops in a zone. This is used primarily to populate the trip history report. If you don't need it, turn it off.
Default property: Visible on map. When you are talking about a high number of zones, only show the important ones by default. Showing everything will slow down the map performance.
Be careful when creating zone based rules as well as with deletion of zones. These two tasks cause extra processing to take place.