I, too, would have to say almost definitely not. As the other poster said, it's too interconnected to the other waterways for them to drain it. They'd have to build multiple dams in order to do so. Also, the Friendships that provide transportation to the Epcot Resorts dock on the far side of WS Lagoon behind China, where the RoE barges are also stored. (This also points out that they'd have to suspend the very popular fireworks show during such a draining)
Plus, there's just no reason to do so. They drain the Rivers of America on rare occasions, but it's relatively shallow (6-8 feet, I believe). World Showcase Lagoon is 2-3 times that deep. Also, the riverboat on Rivers of America uses an underwater rail for guidance, which occasionally needs work. All of the craft in the WS Lagoon is free-floating.
If underwater plant growth or debris build-up happens in WS Lagoon, they'd most likely just bring in dredgers.
-Rob