I think that your "1%" or more would probably wreck each other in the effort to find a carrier strike group to attack. These carriers don't just go around broadcasting their location for all to know. And if Iran did gather 1000 boats in one location they'd be detected by satellite/Global Hawk/Predator UAV in plenty of time to be destroyed in port.
read this article:
http://www.nytimes.com/2008/01/12/washington/12navy.html
the navy is well aware of this serious threat. this type of attack is not as easily handled as you think