Well in WW2 many of the ships carrying troops and equipment were civilian transport and cargo ships converted for a military purpose. Generally the larger ships would be given a simple 5in gun wielded to the deck *the guns themselves could be the obsolete armament of older scrapped destroyers from the first world war* A single 5in gun would provide a ship a chance to defend itself, however the lack of armor and maneuverability of a civilian made ship would be a critical issue in a fight against other naval vessels, but in a convoy with many ships there would be enough firepower to repel a destroyer or 2. It should also be noted that some of those ships were also given an armament of 1 or 2 AA guns to defend against air raids, a few ships were even given sonar and torpedo early warning systems against subs, and early on in the war some were fitted with a rail system to launch an outdated fighter *the pilot had to land in the water due to no landing gear and had hope for rescue*. But still convoys needed solid destroyer escorts and air cover, but in a tight situation had a chance to defend themselves.
In this game however they have less defensive capability than in real life, but they can hurt your destroyer. *not much though*