I would imagine that the fuel store of fission fuel or antimatter would be tiny compared with the Jump fuel (if you subscribe to the idea that they are different). The chances of hitting a reactor fuel pellet would be negligible.
I agree with you in the case of AM plant (though the consequences of an AM fuel hit are so catastrofic that it should be contempled, even if only as a critical).
In the case of fision fuel, to achieve an endurance of 30 days you need 1.44 kl per kl of power plant (2 Mw, if your PP is 50 kl or higher, as surely is in any ship), so, to have a 500 Mw PP (not too large) fed for 30 days, you'd need 360 kl (26.66 dton) of fision fuel, not so negligible, IMO.
As those plants would only be used at marginal early stellar ships, only capable to jump 1 (and barely so), the volume ratio would not be so favorable to hydrogen.
As an example, a 400 dton J1 M1 (our proven fat trader) fed with fision plant needs 540 kl (40 dton) of hydrogen, and 374.4 (27.7 dton) of fisible fuel, and that's just to feed the MD for 30 days. Surely you would need some more energy to feed other systems, and each Mw the ship needs would add 0.72 kl of fisible fuel. And, as such grade radioactives are quite more difficult to obtain than hydrogen, I guess those ships would have more than 30 days endurance, unless they serve only regular routes.
IMPORTANT NOTE: all those calculations are made in MT rules. In MGT rules, the same 400 dton ship would only need 4 dton of fisibles per year (
MUCH more efficient fision plants), against the 40 dton of hydrogen per jump. In CT, AFAIK there are no rules for fision PP, and I cannot talk about other rules sets.