Historically, by deck gun or ramming, or by boarding and scuttling with charges or simply by setting it on fire.
Many crews made a lot of fun out of such "pirate style" boarding.
German VIICs in the med often sank small motor sailboats by ramming, off the Lebanese/Palestine coast. I suppose none of these was manned by british.
British boats did the same in the aegean.
US submarines used flak guns or main guns for sampans, or small arms of the crew.
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