I have used ships similar to what Magus describes, but the other feature I use is Thermal homing missiles. Some of the absolute best hits I have done to NPRs have been via the thermal homing bushwhack. They are GREAT for a port attack. My ship(s) sneak into a system, spot the bad guys, and fire every thermal seeker they have at a waypoint and then scram.
A large salvo of the thermals can do a heck of a lot of damage, especially since they are generally not going to get detected by passives until they are quite close. If you can catch the fleet with no actives (or shields) up, it can be pretty impressive.
Needless to say, box launchers are the way to go. Shoot em all and run.
The big issues with this scenario are A) spotting, and B) speed/endurance.
Spotting stuff far enough away with passives requires BIG sensors, which limits space for other components. Thats the other reason for using thermals, you can fire at waypoints and the firecontrols can be pretty tiny, since resolution really isnt an issue, you just need to have something there, like minelayers.
Speed and endurance are the other key problem. Thermal missiles are pretty myopic, so that means pretty large sensors in the missile unless you have really good thermal tech. That cuts down on warhead and/or speed or both. One way to get around that is 2 stage missiles, but that makes the missiles big, so less payload. The other option is slower missiles with longer endurance.
I usually go for slower missiles with endurance. Since these are usually "ambush" type encounters against slow or non-moving targets, the missile speed is largely a non issue. Ditto for shooting up civilian cargo, they ships are big, and slow and huge commercial engines are pretty hot.
Using these ships in an open space battle can be done, but it can be quite challenging. Since your fire controls suck, and the missiles are slow, the only really successful way to use them is to fire down the bearing of the approaching ships, at a waypoint, that the enemy is going to cross. That means the missiles become "mini-mines" as the enemy literally runs over them as they chase you. Stern shots at a fleeing enemy are usually not worth wasting the missiles on.
Now for the math nerds among us, the real trick is to fire a salvo at a moving target and timing it to arrive in front of them. This is for shots at non 0 degree, or 180 degrees of bearing. Thats exactly the same kind of shooting the subs in WW2 did.