The guest transport boats are piloted by licensed professionals, and they are equipped with vests, but there is no expectation that you will use them except in case of emergency. They are stored beneath the seats. I have never seen anyone take one out for a normal ride.
I also have a strict vest rule for private watercraft, but I look at it this way: these boats are analogous to a city bus. They are for the most part large and quite slow, with very high gunwales, and when you are on them you are NOT dealing with piloting the craft, which makes a difference. I'll let my child ride on a city bus without a carseat, and I'll let them ride on a Disney transport boat without a vest, but with my hand and attention on them at all times. (Now the resort launches from the MK are a bit different; those are really small craft, and though we still don't use jackets when aboard, I'm hypervigilant when I take my kids on board those.)
FWIW, the water on 7 Seas Lagoon isn't that shallow in the ferry channel; that is a big craft with a fairly deep draft. I think that the water in the channel is a little over 12 feet deep.
FTR, children who participate in any of the Pirate Cruise excursions are required to have a vest secured at all times from the moment they are signed in until they are signed out, even when the boats are in dock. The CM's for those are all trained in water rescue, and the boats stay inshore and don't go out into depths where the adults cannot wade.