With the way the naval systems works in HoI4, scenarios like having a flotilla of commerce rading german Type VII's being forced to fight to the death against the entire british Atlantic Fleet will be very unlikely.
Based on what we know, most commerce-raiding fights might look like this:
- A sub or surface raider finds a convoy and sinks it
- A sub or surface raider finds a convoy escorted by a single or a small group of naval ships. Might run away stealthily, might be sunk, might still sink the convoy and escorts (if the raider is something like a Deutschland-class)
- A sub or surface raider finds a convoy but doesn't sink it rapidly or stay concealed, so the convoys radio in for help, aircraft and/or naval vessels patrolling the sea zone join in, see above for what happens next.
Fleets can spread out across a seazone to more easily find an enemy, or they can choose to stay concentrated, with more friends nearby but having a harder time spotting and stopping enemy naval vessels. They can also directly do convoy escorting.
Compare that to something like DH where your sub fleet is sitting where the convoys go, sinking them over time, but always in the fear of being found and nuked by the royal navy (or other naval doomstack).
The system with small ships being flottilas that actually were simulated as a single ship is gone. Now, ships are single units, no matter if they are submarines, destroyers, cruisers or battleships.