Currently, ships, drones, and missiles are held together by magic. There are those cool trusses rendered around components, but as far as I know there is no weight accounted for them. Hopes and dreams keep the armored shell in place and all components stiff and in the same orientation to each other.
I propose for your ships you have to select a structural material, and that some amount of tonnage of material would be required to hold your ship together.
Tonnage of structure required would be a calculation based on:
Ship's total volume Ship's total mass Ship's acceleration Material properties of the structural material selected. weaker materials would need more material, strong materials would need less (but might be more dense and expensive).
This would have an effect to lose a bit of deltaV across the board to account for the structural weight, and would put an acceleration limit on your drone or missile based on its structural acceleration rating.