燃費 is basically a technical term to describe the efficiency of engines or gasoline. A 燃費がいいエンジン can work longer with the same amount of gasoline. 燃費がいいガソリン can make an engine work longer for the same price (i.e., cost efficiency) or with the same amount (i.e., per-liter efficiency).
Nothing surprising happens when this word is used figuratively to describe a person or food. A 燃費がいい人 refers to someone who does not have to eat much to live. This sometimes implies they can easily get obese. 燃費がいい食べ物 can refer to either the cost-efficiency or the per-gram efficiency, depending on the context.
In your context, 忍の ("shinobi's ones") refers to the 兵糧丸 made or used by shinobi. Note that this の is a pronoun (
's one(s)), so the sentence is not about shinobi but about the food itself. And it's obviously about the "per-gram" efficiency of the food in this context. All military rations are supposed to be lightweight and nutrient-rich, but A is saying that the one made by shinobi is especially good in this regard.
If the sentence were 忍は燃費がいい (without の), it would mean "Shinobi don't have to eat much".