What's the alternative? Do nothing?
No: the standard procedure is to demand the boat stop for inspection. If they comply, board the boat, if it, in fact, is carrying contraband (in this case drugs), seize the boat, arrest the crew, bring them back for trial, if it does not, apologize for the inconvenience and send them on their way.
This worked for smugglers and pirates at the time of the American Founding, and it will work today.
If the crew resists with potentially lethal force, applying the same falls under the same sort of exception to due process as the police killing someone who pulled a gun on them.
If they simply try to flee when ordered to stop, damaging the boat with some sort of ordinance that will stop it, but allow the crew a chance to escape in lifeboats, where upon they can be apprehended would be in order.
Blowing up boats, killing all hands, for no reason other than suspicion they are carrying drugs is wrong both morally and Constitutionally.