SCB limits are a good idea in general, especially for small ships. That said, I think a good way to limit them would be to increase their power draw and perhaps their mass (batteries are heavy things

) as well as increased heat generation and cooldown times, so that using several of them becomes much harder to balance out with other ship functions during a battle.
That'd still hit the small ships the hardest, while only mildly affecting a Python or Anaconda that has 5+ SCBs and only ever one powered at a time (until they have to use the smaller ones and dual-fire them). Remember, SCBs were toned down, but it did nothing really to limit that kind of loadout. Making them just worse and worse leads to a situation where a Viper cannot afford the power draw or extra mass of a single SCB, where an Anaconda doesn't care about a few tons extra mass and a or two MW they can spare if they have to.
At the moment there are to relatively unrelated issues, both supported by a third underlying issue:
1. Endless SCB spam during a fight, leading to a battle where the winner is decided by who runs out of shield cells first.
2. SCBs required to recharge bigger shields in a reasonable amount of time.
Point #1 is immediately resolved when SCBs are limited to one per ship. Point 2 is resolved by also improving passive shield regeneration so that it scales with shield class and rating. Shield regeneration pauses any time it receives a hit, so better regeneration doesn't make big shields automatically impenetrable to smaller weapons; and it could be made so regeneration ramps up over time, starting at the current 1MJ/s and then reaching a decent maximum after, say, 30 seconds. This would also improve shield reinitialization times as they are directly derived from shield capacity and passive regeneration.
3. Power plant sniping.
It invalidates armour, hull packages, and over-emphasizes the danger of ever getting your shield taken down. If we assume the mechanic is there to stay at all cost, then armour and hull packages need to be changed to equally buff all internal modules (i.e. not guns and other bits sticking out of the hull). Coupled with SCBs limited to 1, a full battle loadout wouldn't be about stacking shield boosters and SCBs exclusively, but you'd have one good SCB and install hull upgrades into the other slots, plus heavy armour on your bulkheads.
Ideally, imo a protracted fight shouldn't be two sides trading blows and consuming shield cells until one of them runs out cells, their shields collapse and their power plant is quickly disposed of.
Instead, SCBs would be an emergency measure, and getting your shields down is only a temporary setback, they will come back up soon enough so that you may armour-tank for a while, and when the shields are reinitialized, maybe then one uses a shield cell to immediately bolster them again. it's also a battle of attrition, but much more varied, interesting, and not dictated solely by the number of shield cells either side has at their disposal.