If I make this DB edit you're suggesting, which I'm considering, will the NPRs be even worse at fueling themselves than they already are? I'm not sure how they calculate how they distribute their fuel, although I know that they'll move back to a fuel source as soon as they run out.
Yes and no.
If you just straight reduce the fuel efficiency for every tech, the NPRs will suffer badly. However, you can leave the first tech alone and nerf every other tech, and then house-rule for the player race to always research at least one fuel efficiency tech which will in fact reduce fuel efficiency. This will work because the NPRs AFAIK will not research fuel efficiency at all, strange but true.
Of course this leaves you back at square one a bit, since the NPR missiles will still have long ranges, so I would only recommend doing this for a multiple player races game when you can tolerate the NPRs being "boring" as long as there is some potential for thrilling PvP combat.