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Not a naval expert really. Just well-read and, ahem, connected to folks who really know the facts - been there done/doing that.

Best scenario is to seize the vessels in question and commandeer them to a safe offloading point after inspection. Might be a good use for the E-bomb featured on another thread. I understand they make a pretty good flash-bang... Gotta disable the electronics/detonators in case they have a dead-man or doomsday circuit. Gotta kill the perps so they can't manually deploy. Need an assault plan that kills the electronics, kills the ability to manuver the vessel, kills the perps, doesn't rupture any WMD containers. I'm outta my league on the specifics of that mission.

All other scenarios, short of a 1-megaton contact-fused weapon fall short. A 30,000 ton cargo vessel is a mighty robust structure. Add to that the cargo is likely well-protected as well. Water (and all that steel) attentuates the blast and heat effects of a large conventional or small nuke, so I say, go REALLY big, go contact fuse, no airburst (unless it's at 100'). [ remember the Pacific H-bomb tests? Nearby men-of-war were damaged but not sunk. ] Still this is a LAST resort option.

Sinking the vessel with Mk-48s gives the bad guys time to act, even if you hit the ship with a spread of 4-6 wired-guided shots within a span of a few seconds. All you need is some bad guy on the 'phones to call out "high-speed screws, torpedos in the water" and Achmed pushes the buttons. They know they are being tracked, afterall. Launch/detonate on warning is bound to be their orders. (this puts any assault team at risk as well-- die in the sel-destructive martyrs' blasts)

And conventional explosives/ sinking the ships puts accidental release high on the list of likely outcomes

Second scenario is to disable their propulsion when they are mid-ocean and pursue option 1 above

Scuttling in shallow water would seem preferable to deep water, so again, the cargo could eventually be off-loaded.

Scuttling in deep water raises the specter of eventual catastrophic release due to corrosion or pressure rupture.

Anytime you have a large concentration or WMDs, seizure is the best option, followed by 'long' duration plasma-temp incineration. Dispersion by blast is not preferred, 'cuz you may not get it all, and radioactivity is not consumed in a chemical reaction like incineration.

So, the issue is not really that the WMDs are on a ship (allegedly) but that they are concentrated and hidden and could be dispersed or delivered prior to safe seizure or destruction.