I don't think you're "buying" them (unless you're "buying" your starships and equipment also, which seems an unduly harsh way to run a space navy!). You're using a nebulous "currency" somewhere between money and honour. Think of it as the Starfleet Influence you've built up, and your ability to acquire stuff from fleet resources or have stuff bought from Starfleet accounts.

On a related note, I find it quite odd we can't replicate the damn things. Even if I had to pay 120% cost, I think it would fit with the mechanics. We already lose an additional 20% value by selling stuff to our replicator. It should make sense to cost us more to replicate some (not all) items from it.

I do not think that model holds up very well either. Imagine you have a green-behind-the-ears captain. Nothing to his name, no commendations, no respect. He comes into spacedock with news of a planet in dire need of medical suplies. Quartermaster takes s look at his service record, is unimpresed and says "Tough ****ies, you're not important enough to request that sort of help for a backwater planet." Not very much in keeping with the spirit of Starfleet imo.

If anything these should be simple fetch missions, where the commodity to be brought back is free.