It would be nice to have to pay to upkeep the military units to prevent spam of them and encourage growing the colony to support a bigger army.

I've thought about adding some sort of upkeep system where you had to continuously supply the military with ammo. In the end I made a decision not to go this route because it didn't fit well with the design philosophy I had for this mod. But I'm open to revisiting this decision at some point in the future.

I do get your point about unit spam though. My question to you: how would you implement an upkeep system in a way that wouldn't feel too constraining or unfun?

It's also possible to add a sort of army limit instead of upkeep, which depends on the colony's population. Or maybe go down the RTS-like path, where you need to build specific buildings to raise your army limit. That would prevent spam and encourage colony growth without upkeep mechanics.

Maybe have military units add unregulated supply? That way we're encouraged to build a stronger economy to support a bigger army?

Depends on how this can be communicated to the player and how easy it would be to implement.