The only reason to ever have 99 or 100 zones up at the same time is if all 99 players you had in your server tried to zone all at the exact same time... If you have 10 to 20 people playing I would recommend having only 10ish zones up (IF that many) Just experiment and see if anyone gets booted off because of lack of zones, I think you will find that you will NOT need tons of them... Unless you have more than 100 people on at the same time...
Think of zones as websites. If you assign each unique zone a port any player who goes to that zone will access that same port, just as if someone were to access your web page.. That web page has the port ID of 80 (typically), and yet everyone who visits it will be accessing it through that port... They are NOT assigned that port individually (the web surfer), it is the site that they access that is assigned that port so that their network or ISP (to make it simple) knows where to find it (again to make it simple).....
Hope this helps...