They are strike fleets so they sit in port till your patrols find each other. Or one may be a naval invasion fleet that your strike fleet intercepts. The point is not to patrol with main fleets as that wasn't done historically.
In RL the BB's used their 5 inch guns against escorts and didn't use their main BB guns. Numerous reasons for this as you also pointed out.
One of the problem is that actions in real life did not work like what is commonly thought. Destroyers would not stand in between two battleship lines... they would just obscure and be in the way and risk being sunk. Once capital ships got into firing range with each other escorts would not be used that way. They might help a battleship escape by running interference, flanking etc.. Destroyers rarely fought each other either, not decisively anyway.
No sane captain would take a Destroyer into firing range of a battleship unless there was some really good reason to or they could do it from a position of strength so they can get close enough to launch torpedoes and disrupt disrupt the ships movement and with some luck hit it.
Real naval battles was not fought the way they are depicted in the game. The role of the destroyer was not screen capital ship against other screens, they were there to screen against submarines, scout and run interference. They are used to gain positional advantages on a slightly bigger scale. Torpedoes on destroyers are more as a self defense weapon against large ships, not a weapon meant to attack as means of doctrine in that sense. There obviously were slightly differences between nations and Japan had a bit more aggressive stance on usage of torpedoes, at least before the war. This changed rather quickly when they found out how important the airplane was. The Japanese were as convinced on Battleship doctrine as anyone else before the war.
There was a reason why the US reduced the number of torpedoes carried on their Destroyers as the war went on.