Super Freighters sound nice on paper - bit longer build time, but much more capacity than a standard freighter.
But for a lot of purposes, they are too big. You don't need a super freighter carrying resupply to the ships in the CBZ - the ship would be mostly empty. Even our forces in the GBZ probably don't yet warrant a super freighter.
Look at the actual loops of transportation we have. How many of them are accommodating three or four existing freighters? Superfreighters could take the place of about two of them. Unless I'm misremembering, that includes some supply routes fairly interior and secure in our space.
EDIT: Two more points:
1) We may be able to arrange a 'quid pro quo' where Starfleet superfreighters haul bulky goods for member worlds along with our own supplies, reducing the strain on their transport assets and easing resentment if we conscript one of their smaller, lighter freighters to resupply remote outposts that the superfreighter would be wasted on.
2) The superfreighters will be
very helpful in carting massive quantities of supplies and spares to forward depot locations in the event of a war mobilization when we suddenly have a lot more supplies to move around, and very large fleets that individually consume exceptional amounts of supplies. Remember that we're not just concerned about making up the immediate shortfall in Starfleet transport assets, the one we cover by drafting member world transports. We're also worried about wartime issues. Remember how we needed like... I don't remember exactly, a dozen freighters and cargo ships to supply the fleet we were using to fight the Licori War? A superfreighter or two would have been very handy right then.
A superfreighter can do two things a smaller one can't: it can load cargo for a distant destination while still having enough space to also load cargo for intermediate destinations, and it can load considerably larger items.
Like, for example, replacement nacelles for damaged starships.
That latter issue doesn't seem to be a problem for us. And honestly, a competently designed freighter built to the same scale as a
Constitution-class starship should be able to carry a nacelle for any ship we have or are planning, including an
Ambassador.
That sounds nice in theory, but it's quite possible that 1 freighter worth of transport capacity needs to be 'on station' for optimal efficiency, as then you've got a cargo manifest and automated systems ready to drop whatever the engineering crews need to work with right now while keeping local space from being cluttered by floating containers.
This sounds like a concern that the engineering team might run out of space to put things in...
in space.
Space is
made of space. The one thing you're not going to run out of in space is big empty places to put things.