Not all large ships had amazingly strong armor like they present in the game. Some had to go very fast; the strong armor had to be sacrificed for the speed. And, if they turned their prows to the smaller ships, all the small ships had to do was move. Small ships would out-maneuver the larger ships, and not always had smaller cannons. You could fit a pretty big cannon on a light ship if you had to.
These are medium war galleons. If you had a light galleon (the real ones.. Not the fake ingame ones.) It could take this out if it got close up to it and the upper cannons of the warship could not reach. Half of the broadsides would also be unable to reach the light.
I'm not saying light ships ALWAYS win against wars. There's a reason they created warships; to win. But, if a light had no choice, or, even a medium merchant-size ship had no choice, it has a good chance to take out a warship.