I think the biggest things are weight, drag and maintenance. If you're building a boat for play, it's not a big deal. If you're building a boat for racing, however, the extra weight can screw up the balance of the boat. What you have to remember is for every ounce you have hanging off the back of the boat, you have to have weight to offset it in the front. This can be accomplished in many ways, one being to move the motor forward. That will, however, make it harder to access the motor so you're trading cool for access in this case.
Now, let's talk drag. Again, for a play boat, no big deal. For a race boat, however, anything that hangs down into the water makes more drag to overcome. That equates to a slower boat due to the added drag, a heavier boat due to more power being needed to overcome the drag of the extra blade by going with a larger motor and fuel tank or shorter run time by sticking with a smaller tank and larger motor. Again, you're trading speed, weight or time for cool.
You're probably wondering how maintenance can be an issue. Using a twin rudder will actually will make setting up and maintaining your boat harder:
1) To replace the prop or drive shaft, you will have to work around two blades instead of one, making access much more difficult unless you remove one or both blades every time you need to access the prop or shaft
2) Two rudders mean twice and many bushings/bearings to have to maintain or replace when compared to a single rudder set up. That means twice the expense as well.
3) Two rudders also means aligning them every time you have to remove them or do anything to the rudder linkages. If they are not properly aligned, you will have to deal with a boat that is hard to drive since the rudders will be fighting each other. The best comparison I can give on this is a car that needs an alignment. It won't track straight so you're constantly having to correct for drifting and it causes the tires to wear faster. While the rudders won't wear as tires on a car do, the other effects are still there.
Are you sure the "cool" factor is worth it?