Completely get rid of the ammo function of SCBs, limit the equip amount to 1 or 2. Turn it into a rechargeable battery heavily dependent on SYS power/distributor grade. Changes the dynamic of combat and makes the pilot switch to the defensive to recharge their SCB once used etc. Essentially turns a pot to a cooldown (dependent on power management/module grade). That way you don't have to deal with the overcomplication of boot-up times and heat sinks. Simple.
As for heat generation, look at the FSD. I can't fathom the amount of energy dumped into a shield eclipsing the amount of heat generated to charge a jump in nearly the same amount of time.
I fail to see how that implementation would be any less convoluted in terms of balancing.
- You wouldn't have to restock, so it's undeniably simpler for the player there.
- You have to balance how fast they recharge, with how much energy to the SYS, depending on generator, distributor and shield cell size. Not any simpler to balance nor any less convoluted than discouraging spamming with negative effects. It's a "use as often as you can" affair vs. a "think if you can afford to use it" affair from a player's PoV.
- You are proposing the introduction of an artificial limit for how many SCBs may be equiped. That's not intuitive either if it's greater than one.
- How would multiple SCBs (2 in your case) be handled? Could they be simultanuosly powered, both recharged, but one deactivated and then reactivated when the first one has been used? Will the reactivated one already be readily charged? If not, that's no different than the boot-up time they are introducing now. If yes, that's what SCB spamming is like now, just that rather than giving the player a good reason not to do it, its limited with an artificial max number of SCB modules.
Attaching notable heat generation to something that logically uses a lot of energy within a short amount of time seems more logical to me than introducing an arbitrary, greater than 1, limit to how many of modul type X may be installed. The first option can be explained with the already twisted game logic, the latter is a number to learn by heart. The game lets your ship fry itself rather quickly in silent running too.