Hello,
unfortunately, for NPCs weapons are mapped directly from NPC XML, there is no way to change NPC weapons from scripting.
So, it makes sense to make a few NPC XMLs with particular weapons (per weapon type, multiple tiers). Giving too much choice to the player is something I would recommend to avoid as it might easily overwhelm the player. Consider having only a few presets for drones, the code generation for it is overcomplication and simply abusing the idea of XML's.
But you can modify NPC shield stats/properties, such as damage - as you found out, with the IMCache.
It's not recommended for mods to call ship.SetEquipmentCacheValue() - this method is intended to be used only by IMCache when it calculates "ship cache" (it combines stat values and bonuses from various sources and then applies them with ship.SetEquipmentCacheValue()). If you call this method directly you will overwrite the value set by IMCache (and if IMCache calculated any time later, it will overwrite your custom value). It's better to simply provide these values to IMCache instead. As you wrote, there is the CalculateShip.js script - and I think modifying it is the best way to do this.