We don't know what happens with the souls once they're eaten. What about the other Dragonborns throughout time who supposedly slew Dragons and consumed their souls. These are supposedly the same Dragons.
What happens when you eat food. That food is not technically, permanently gone, if you know what I mean.
My understanding is that when the dragonborns die, the souls return to the dragons or something.
With your food anology, it would still be like the circle of life, except with dragon souls.
I think that gameplay wise, it would've been better to keep the # of dragons limited to how many dragon burials there are. They wouldn't be so [censored] annoying, and the less dragons there are then the more special each fight would be. The main selling point wouldn't be gone this way, as the main quest can still be exactly the same, except with less random dragon attacks.
Also it would limit how you spend your dragon souls, instead of being able to "buy" every shout and still have tons of souls left. This would increase replay value and strategy.
And just because this is a fantasy videogame doesn't mean that there can't be
any logic whatsoever.