I suppose someone could could try to recover it someday - but get it deep enough... Of course, if its intercepted mid ocean then you may not know for sure who it was going to.
But, it seems odd that you would track this shipment out on the ocean (fairly easy I would guess) but let it arrive at a port with trucks and rail cars and other ships going every direction and not be concerned on if the whole shipment is going to one place, several places, or where? But... they may have had “on the ground” information to minimize them losing it. (Its a Brand X weapon, the only Brand X facility they have is located at ....)
Alternately, someone managed to slip a tracker or homing beacon on the thing (or it may have had one already and someone figured out how to track it) and they wanted to see where it was going to go.
Otherwise, yeah, disposing of the boat over some of the oceanic trenches would be the best thing to do.