When they went from the side drain to the stern mounted drains, the water instrusion issues just about went away.
Like fastcat said, some people have added the Rabud ping-pong ball drains. I have had no water intrustion issues at all on my 02 2400V with the standard stern drains.
We have a 99 2200V at work that has the side drains. We use basic plugs on the drains to keep the water out.
Here's a link to the MHPC website forums...
http://www.mbcboats.com/fusionbb/