Ships were first armed with cannon in the 15th century. At this time, no disctinction was made in the design of military or merchant ships.
The merchant ship of choice in the 16th centry, the carrack, was armed.
The East Indiamen trading ships of the 17th and 18th centuries were heavily armed, able to slug it out with ships-of-the-line on equal terms.
The 19th century saw the development of the clipper, which relied mainly on speed to avoid piracy. Also, privateering was outlawed in 1856 through the Convention of Paris.
Armed merchantmen were used extensively in the 20th century, by both sides during WWI and WWII, in both defensive and offensive roles.
The current situation with piracy in not new or unique. It is just a different geopolitical climate in which it is has taken root. Having to fight to protect your international trade is an enduring historical reality. I can't see that changing anytime soon.