I believe that a good portion of Seven Seas Lagoon is deeper (or at least consistently deeper) than Bay Lake. When the MK ferry boats have to travel to the maintenance area/dry dock at the north end of Bay Lake, there's a very specific channel they have to follow that's been excavated out for them. I've seen a video somewhere out on the Internet of a ferry getting stuck in shallow water in Bay Lake because it drifted away from the marked channel.
From what I was told - and again, it's not a verified source, but I assume a ferry pilot would know the depth of the waters he is navagating, and the draft of his vessel - SSL is deeper on average than Bay Lake, but its on the order of 20-25 feet at its max. According to him, he has also never seen it dredged. The ferries draw about 6-8 feet - which seems a bit shallow to me, but then I am no expert.
I can see that when they have to go into dry dock, the lake gets shallower than 8 feet near the shoreline and they have to follow a channel into the drydock approach.