I misunderstood the topic, I guess my suggestion’s kind of pointless. Didn’t thought it’s about having all the customized weapon themes applied in a mission. Sorry about that.
I had another idea though:
Themes itself will be purchasable at the Heroware as a separate item. The symbol itself is a designated weapon with small paint palette. Use the image below as a reference but change “Laser Cannon” to “Weapon theme (Laser Cannon).” The price is definitely lower than the weapon itself.
Sample list item:
Weapon theme (Ion Blaster)
Weapon theme (Neutron Gun)
Weapon theme (Laser Cannon)
Weapon theme (Lightning Fryer)
etc.
These are purchasable having the current weapon’s default color, unless customized by the player afterwards. There will be shops that offer customized color themes as well with a designated rarity.
Next, as you said before, a dedicated submenu will be added in which the player can customize the weapon theme further. In case you bought multiple weapon themes for the same weapon, you’ll need to choose one to be used in-game (works as the “flagship” for ships). This allows the player to own multiple weapon themes not worrying about changing it everytime to match up the current spaceship they’re using or other applicable scenario.