It seems like if you can get the reactor working then you're floating right on top of all the fuel you could ever want, provided you're doing hydrogen fusion.
Fusion fuel is so compact, there's really no need for that. To get an idea of it, deuterium is less than 0.1% of the hydrogen in water, and there's enough in your morning shower to provide all your energy needs for a year.
Nuclear aircraft carriers go thirty years without refueling, and fusion could easily do the same.
Mounting a fusion reactor (largely automated - these ships have a skeleton crew) on every big ship seems ambitious enough, why would you...sure, why not, package an automated deuterium fuel refinement facility in a box on the ship too. In another ten years you'll be getting them in Christmas crackers.
Nuclear aircraft carriers go thirty years without refueling, and fusion could easily do the same.