I don't see why not, you had piracy in the 18th century as well and those merchant ships armed themselfs (obviously not to the teeth, as pirates, speed was usually their main defence). The technology has improved, but the pirates never left, why should merchant vessels stop arming themselfs then? It's not like the pirates got any more civil in those years.
Sure they don't need rows of cannons, afterall the pirates don't travel in the same big boats but small speedboats, but a .50 machinegun would help a lot.
Ofcourse, only when they go through pirate waters. If not, they shouldn't arm themselfs.
PS: As for giving the untrained crew guns, no, you've got professionals for that.