They are treated as cargo - the key is having the "open space" to transport them - ie nearly empty supply/ordnance storage bays.
Not sure how well remote drop/load orders will work with supplies/ordnance though.
For the Balance Mod, consider having your colony ships carry surplus supplies/ordnance so the colonies they found have an ok base to refuel a few ships before a Supply Depot of two can be built in the system.