That weapon of choice for the armed merchantman employing organic naval commando units during a time of crisis or overt hostilities the submersible boat? The "mother ship" carrying the frogman/under-water demolitions team/naval special operations unit and doing so in a surreptitious manner.
A submersible boat such as the Russian Triton-NN or the Swedish SEAL carrier!
"SEAL Carrier operates in three modes; surface, semi-submerged and submerged."
Has all the attributes of the conventional diesel/electric submarine:
* Takes in water to submerge, expels that water using compressed air to surface.
* Operates on the surface using an internal-combustion engine.
* Operates when submerged using a battery-powered electric motor.
Swedish SEAL carrier in action. While surfaced has the performance of conventional speed boat. Just above the diving plane you can a man emerging from the hatch and giving you a sense of scale. Click on image for a large view.
"Launched from a surface ship ["mother vessel"], SEAL Carrier vehicles transit at speeds of up to 30kts [knots] on the surface before switching to submerged mode for a covert final approach"
Also has a snorkel capability. Allowing for the internal-combustion engine to be used for propulsion in the semi-submerged [deck "awash"] status. Batteries conserved for that totally submerged and most secret portion of a mission. SEAL CARRIER "WET" ON THE INSIDE DURING SEMI AND TOTAL SUBMERSION!
See this YouTube video of the SEAL carrier in action: "Special forces The Seal carrier on the Swedish Navy Military HUB