Today, I would think free missiles is not a bad idea, given that most are unsuitable for endurance fights players tend to get caught in within the campaign, while the regenerators are inferior to the Converted Hangar and fighters combo.
But once the loot bug gets fixed, free missiles would be unbalanced by perhaps enabling missile-spamming chain-flagship fleets. That is, player deploys a flagship, fires "all the missiles" at enemies (to overcome defenses), kills a few ships, then retreats that ship. Repeat with the rest of your fleet one ship at a time. If that does not kill everyone, full retreat to end the round. If enemy wants to fight round two, repeat the missile spam. (If enemy runs, auto-resolve to get your free kills.
Currently, full retreating is punishing because player forfeits all loot, but not XP, from ships killed that round, even if player ultimately wins the encounter. But that was said to be a bug, and will get fixed. With loot bug fixed, a full retreat to take a timeout (to stop CR from decaying and/or reload missiles) becomes a viable strategy instead of a huge loot tax.
That would be an incentive for limited ammo weapons to regenerate, to discourage full retreat timeouts if that proves to be very effective.