Cruise missiles are in kind of a rough spot at the moment, with the existence of Tusko-Bs and Piledrivers, making them superfluous in most of their intended roles. The ultimate solution to TBM spam will probably be a combination of revising their guidance, launch requirements, and the introduction of new threats and counters. That said, I think remixing some of the aircraft loadout options in the short term might help to ensure all of the game's existing cruise missiles have a use case, even if a narrow one.
1: Make AShM-300 Medusa-exclusive
The AShM-300 is arguably the best cruise missile currently in the game- the problem is that it also makes all of the other cruise missiles obsolete. Sure it's the most expensive, but it's also the most effective (the additional cost and reduced warhead weight compared to the ALM-C450, its closest equivalent, are almost meaningless). Restricting it to the Medusa would reduce their spammability, and also give the Medusa an additional niche as a cruise-missile carrier/ship-buster, without totally gimping their maximum volley size.
2: Make ALND-4 available on aircraft pylons which can carry Auger-2P (or if that encompasses too many aircraft, at least make it available on one of them)
With the Piledriver TBM-N as an option, the ALND-4 is kinda obsolete on the Darkreach. However, I think it would have a useful niche on smaller platforms both due to its moderate 20kt yield, and ability to be launched at range, which are nuke features only available on the Darkreach atm.
3: Make AGM-99 available on larger platforms (Medusa and Ifrit)
Currently, the AGM-99's real advantages are its low weight and cost- this would be great for cruise missile spam... except it's only available in small numbers on the Revoker and Vortex. Making it available on Ifrit and Medusa with greater capacities (8-10 depending on how mounting space and weight) might encourage players to use them more often, especially if AShM-300s were curtailed in availability.