Arming the system does not use significant hydraulic power, and they would be armed on approach while the engines were still windmilling enough to produce enough hydraulic power for adequate flight control (if you were ditching with engines not running).
The autobrakes would not actuate unless a bunch of gear and wheel sensor mayhem occurred upon striking the water, but I believe this unlikely scenario is what Boeing was accounting for with that advice/step in the procedure. Given the logic for autobrake actuation, I agree it's very unlikely for autobrakes to be triggered.