You only picked up on one exclusion, there are 3.
Here's an excerpt from RCW 46.37.340 (
(3) Brakes on all wheels. Every vehicle shall be equipped with brakes acting on all wheels except:
(a) Trailers, semitrailers, or pole trailers of a gross weight not exceeding three thousand pounds
(b) Trailers, semitrailers, or pole trailers manufactured and assembled prior to July 1, 1965
(c) Any vehicle being towed in driveaway or towaway operations, provided the combination of vehicles is capable of complying with the performance requirements of RCW 46.37.351
I think that (c) is the important one. Here's a link to RCW 46.37.351. Basically, it says that if your truck/trailer combo can generate enough braking force, then your are exempt from the "brakes acting on all wheels" requirement. Here is the summary definition of "enough force" for a truck with trailer:
  • generate braking force greater than 43.5% of gross weight
  • decelerate faster than 14 ft/s^2
  • do 20-0 mph in less than 40 ft

I don't know for sure but I'd wager a bet that the boat manufacturers have analyzed the braking system and determined that brakes acting on only a single axle can meet this independently of the truck (i.e. the brakes generate at least this much force on their own and don't depend on any part of the truck breaks to meet this requirement) I can't figure any other way that the boat manufacturers could legally sell them otherwise.

If I were in WA, I would feel comfortable that my Moomba on its tandem axle trailer with single axle brakes was legal.