Again, CORPORATIONS. Profit margins at all cost. If corporations can cut off one part of the cost, they take it.
Second, notice that there aren’t all that many agriculture pods floating around in space. You really only seem to encounter them in mission sites and deadspace complexes and they are too small to meet the needs of entire space-borne civilisation. What little they do have is supplementary.
In space itself, in order to save space, they wouldn’t be raising livestock out there. It’s going to be mostly vegs and tubers, especially potatoes and beans. If anyone wants meat, the cheapest solution is going to be flavoured protein paste. So, to get lots of protein paste for the cheap (and legal), they will need to process potatoes and beans (and excrement. All of those need to end up somewhere). So much trouble.
Now compare to some bloke with a vast collection of corpses just dropping them corpse in the corporation hangar and asking for a very fair price. If someone thinks that they can shave off a couple percent by using corpses someone is selling to them on the cheap to make these pastes, they take it.
Corporations have no morals, only balance sheets.