The problem is that drones have zero collision box, so ballistic projectile weapons are unable to collide with it. That means shotguns and cannon rounds will not hit a spawner/arachnid egg/wasp drone and simply continue flying past them.

I have tried to add a collision box to drones, but the game doesn't let you have combat drones that have non-zero collision box.

The solution I can think about is changing the type of entity used to a regular unit instead of a combat robot.

Stationary machine gun turrets in K2 kill drones without problems.

Replacing the drones with something will be a problem, because. only this object has the property of spawning something after the expiration of the lifetime.
In the case of Arachnids, drone-egg immunity to AoE damage is a planned feature. But the fact that they cannot be shot down from a machine gun in K2 is not what was intended. I'll think about what can be done.

For now - use turrets

I've discussed this phenomenon with folks at the official Discord server, and concluded that the drones simply need a collision mask in common with the projectiles to be able to be hit by those projectiles. My conclusion of needing to replace the entity type is a mistake, sorry.

Weapons that instantly hits like regular guns and turrets, and homing projectiles work fine against them, yes.

I haven't found a way to give non-homing ammo the ability to shoot down drones. This means that that K2 players with "realistic weapons" will have to use their drones, or a rocket launcher in battles against arachnids without the support of turrets.

I have patched my copy to fix this issue by requiring Combat Mechanics Overhaul and applying the "flying-unit" mask to drones.

As far as I have checked, adding a Combat Mechanics Overhaul by itself does not solve this problem.
Even though it already assigns a "flying layer" to drones and projectiles.

I'll see what can be done with that in mind

At the very top of DroneUtils.lua, I added:

local flying_layer = collision_mask_util_extended.get_make_named_collision_mask("flying-layer")

then, after drone is defined but before returned in droneUtils.makeDrone(), I added:

drone.collision_mask = collision_mask_util_extended.get_mask(drone)
collision_mask_util_extended.add_layer(drone.collision_mask,flying_layer)

then I added Combat Mechanics Overhaul as optional dependency. This patch correctly adds the required collision mask for compatibility with projectile weapons.