I am uncertain if i understand that.So in answer to your question:
"Should it really make a strength difference for a ship to carry it's own weapons + ammo than carrying smaller vessels with weapons and ammo?"
Yes, you save at least by 35-40% on fuel just from having in-flight refueling, not to mention all the other stuff I've already mentioned.
Even if the Carrier is out of range of friendly tankers, friendly depos and cannot sit outside the field of battle refining fuel while it is stationary. Just from the fuel savings of in-flight refuelling alone you could still see a saving of 35-40% fuel use... and fuel savings could, using a realism argument, be represented by higher DPS.
The total amount of fuel consumed in a battle is less is what you are arguing, right?
But I think you are saving 35-40% of like 1% of fuel use, because the strike craft are a negligable amount of mass compared to the carrier.
Or are you suggesting that your Strike craft are so incredibly multi-purpose that they can be used for refueling the carrier? I highly doubt we'd ever consider using F-22 to get fuel for an aircraft carrier. That'd need to be specialised vehicles.
But what about the hangar space, the more enhanced maintenance and all that's required for it?
If you want mega-multi-purpose strike craft, they necessarily lose efficiency, too. Unless you assume it's iron man's nanotech that can form any complex machinery from nanites, including thrusters and weaponry, etc.