Well, there are a number of things:
- Shortages don't have to be just for food, after all. Since both ports carry (almost) every type of good in large amounts, a shortage of any good can be capitalized by shipping stuff from one of the ports to the other.
- Food shortages can and do occur, however. Most notably trade disruptions from the Knights Templar. And even player-driven ones if they buy out all the food (as I once did, delivering food to a neighbouring star system and buying out all the food).
At this point I've honestly stopped trading in Thracia out of choice because it feels too much like cheating. I make far, far more credits (measured in both in-game days and real life time) doing Babylon-Byzantium runs than I do with any other run. Or bounty-hunting. There's also no risk to them, unlike real interstellar trade routes, which have not only marauding pirates but the risk of a shortage ending before you reach your target system.