This works great, if one can get the merchant ship with commandos in the Canal. In a strange way, on this operation, the last 100 m to the target may be the easiest part. For the limpet mine option, I would be tempted just to hire some locals, or try to have a submarine unload 10-20 Japanese divers on the Panama coast on the first day of the war.
But if I could get a merchant ship through security that was poorly searched, i would just have 30,000 lbs of explosives deep in the cargo hold that I would explode. There is no reason to get cute, if the security is that poor.
The security was not that poor. The US searched every ship, to the level of confiscating handguns and cameras. Put a pilot and escort crew aboard, offloaded the whole crew in some cases. Turned back ships with any discrepancy in their cargo manifest. Non US flagged ship sometimes sat for a week or more while they were searched. Even US flagged ships were searched fairly closely. If they found 15 tons of explosive that were not on the manifest the ship would not go anywhere near the canal.
Many ships had their whole crew and passengers get a free train ride to the other end of the canal zone in a blacked out train, while the assigned pilot and canal crew took their ship through the canal.
This would not be easy if it is even possible.