You could add an equipment that functions similarly to the nanobot gun, but frees up the gun slot and maybe saves on ammo. For the ammo requirement, you could either let the ammo be inserted into the equipment (the heavy tank mod does this for diesel engines), draw from the main inventory, draw a lot of power (create bots from energy/use structured energy as bot equivalent, lore-wise) or remove it (nanobots eat the sand under your feet to replenish them).
Why?
The nanobots just work much more comfortanbly than the normal ones IMHO. You never need to wait for them to catch up, they can't be damaged and can repair walls without extra repair packs (though this can be a disadvantage, if mods add faster repair packs). This makes them still useful later in the game when you already have bots, but blocking one or two (if you also want a termite gun) weapon slots is a big downside.
Lore-wise, it makes sense that later in the game you can unlock the replication limit of the nanites (Nanite Replication Hacking as prerequisite for Nanobot Equipment), internally mass-produce them and fire them from the pores in your armor.
Technically, I'd wish for:
Contructor Nanobot Factory: 2x2; fulfills role of builder nanite gun; multiple factories increase build speed
Termite Nanobot Factory: 2x2/1x2/2x1/1x1; fulfills role of termite gun
....An upgraded version might 'burn' trees for armor power, allowing you to recharge your batteries while attacking forests.
Logistic Nanobot Factory: 2x2; Insta-deliver requested items to your person if provider chests are in range
Nanobot Communication Extender: increases nanobot range
Military Nanobot Factory: 3x3; space science required; better personal laser defense with small AoE, somewhat higher damage and affected by com extenders and termite nanobot animation (but in red).
....Upgraded variant: instead of high rate of fire, small AoE this Factory releases swarms of nanobots (similar to nanogun fire effect) that work like stronger poison capsules.
........Further upgraded variant (of questionable balance): Biter Gray Goo Mod - makes military nanobots reproduce when attacking biters, converting them into running nanofactories for the few frames that they stay alive. Clouds are good against spread out enemies (large radius) and stay around for ~30s, while normal mil nanobots quickly jump to nearby targets, obliterating the largest clumps within seconds, but having problems with isolated targets.
Also, an early game upgrade (red+green) that makes the clouds you can shoot out of your gun slow/damage biters (significantly worse than capsules) would be nice.
