I have found scant material on these but my impression is the weaponry is aimed at tackling armed merchants. In theory they might be pitted against the lightest of ASW patrol vessels, The later development was enthusiastic thus Surcouf, HMS M1, M2 and X-1, and the USS Nautilus/Narwhal. Again, I think the theory is to have a weapon capable of obeying Cruiser rules but even better capable against the armed merchants and maybe the usual escorts. It might force a disproportionate investment of heavier ships as escorts, draining the battle fleet of scouts. In any event the Treaties saw enough threat to squelch it. Without them I think this type gets way more investment and I think we see more attempts to put aircraft to sea in submarines. The various navies were poised to pursue this even if a dead end.
I can see this mindset. The need for airplanes as scouts for submarines is compelling, and there is a huge advantage in being able for force convoys to also have a couple of cruisers protecting them. Without the treaties and with some nation pursing submarines more seriously, then I think the solution falls either to specially built cruisers for the role or AMC if doing it on the cheap or last minute. The Japanese built one or two of these ships, but when not used in the intended role, the ship was a port queen without a job. You basically need 6 guns of the 6" to 8" range and enough armor to easily handle 5" guns and massively long ranges. The back of the ship carries the 6+ airplanes needed. And you need submarines that can keep up with the ship and have very long ranges. And you need to deal with the electronic emission issues associated with coordinating the group.
So since we are on German subs, you basically need to not be so worried about tonnage and built 5 very long range subs designed to operate with the surface raider ships. Then at least in theory, these 5 subs plus the Graf Spee can unleash untold havoc in the South Atlantic. And the Japanese version could have done the same in the Indian Ocean. It is debatable if these combinations work. Strong supporters like me will say in the right conditions, yes, for a few months at a time.
This ship may have been seen as you say. Too heavy for a AMC, too long range for escort destroyers, and the torpedoes can handle cruisers. Probably the best way to tell is look at the range. If designed with significantly more range (say the converted Merchant Subs), then this ship may well have been designed for extended operations well away from Royal Navy bases.
Now what I really think works just using a regular warship who operates with subs, and this would take prewar practice. If one thinks something like the Bismark breakout where it is at least coordinated with U-boats, then it might be a different game. Or if the Japanese had been willing to risk a heavy cruiser with a handful of subs on a long range mission to try to shut down some shipping lanes. It is just that most admirals will not be willing to risk "war winning ships" in anti-freighter operations.