It’s not just ammo/charges that are affected, but items like an MTU or other deployable structures, so this is too broad to have for example charges segregated into a different hold.
Second, splitting the cargohold into smaller units would lead to more wasted space. For example, if you set aside 100 of the 480m³ cargohold of a Vexor and only use, say, 50m³ for ammo, the other 50m³ would be unusable.
For now I think I’ll help myself with using cargo containers. As in, placing the loot in there and keep the readily accessible items (like ammo and scripts) outside of them.
Still, the ability to lock items would be definitely a “nice to have”.