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.
That makes the most sense.
Assuming there’s no radiation smoke rising from the site it would be kinda telling. If I had planned the raid, there would be a small nuclear radiation leak with the smoke because the best way to set back the program a couple of decades is to make the area radioactive and they’d have to clean it up, not suspecting the nuke was stolen.