On paper, it sounds like a relatively reasonable idea to have people buying siege ammo off actually friendly bases.
In practice, this would be ineffectual/impossible to balance.
Virtually no factions have rephack maximums towards each other except hostiles or undockables. So tying it to rep would only....force people to get bribes? Which is not really a relevant gameplay or roleplay process that we need to force more of?
If you say, max hacked every single ID in the game dramatically towards other IFFs in order to achieve such a rep-based ammo system, reducing the availability further down from simply dockable bases would cause a really unpredictable situation with possible "black holes" where bases are effectively immune to attack, and it would be extremely hard to determine where and for which IFFs they would be.
No, this just doesn't work out at all. Don't try to overcomplicate things.