I'm opposed to the drone strikes, but there is a clear difference here. In the case of these fishy vessels, they could be detained and boarded. It's not really a high risk situation, and it's something the Navy and Coast Guard are trained to do.
In the case of alleged terrorists being targeted by drone strikes, it would be risky in many cases to try to apprehend those individuals. They are in foreign countries or parts thereof which are not under U.S. control or control of an ally.
It's only not a high risk situation if they are in fact honest fishermen. If they were drug smugglers, I would expect them to also carry weapons. Boarding seems risky to me.
It's something routinely done, with ample ability to defend themselves against a single speedboat. They can always shoot a missile at the boat after it starts shooting at the coast guard; the outrage is that that was the first thing.
In the case of alleged terrorists being targeted by drone strikes, it would be risky in many cases to try to apprehend those individuals. They are in foreign countries or parts thereof which are not under U.S. control or control of an ally.