This is probably a result of them taking away the unlimited cargo glitch. Basically, you would be able to loot for hours and no matter what you got, you'd keep all your royal chests.
Correct, even if you loot for hours you still get to keep all the loot that you earn.
My point being, this is
not a glitch so please don't call it one. In fact, it is the norm in the game and has been since the very first inception of looting in the game...even before hunters, we'd still keep both cargo and loot chests/pouches, and then materials worked the same way. You sink it, you keep it. The only time you don't get loot is when there is no room in the hold and a lesser cargo is all the sunk ship has to offer (ie if you have a hold full with minimum treasure chests and sink a ship that only has cargo crates, you loot nothing since cargo crates have a lesser value than chests).
However, the loot itself was correct before and by my understanding is set to return. You need both materials and gold for ship upgrades and it already takes well long enough to upgrade as is, hence we should be able to loot both gold and materials, not just one or the other. In addition, as mentioned above by others, if we sink the ship, we earn the cargo looted. There is no sense in taking it away just because we continued to sink other ships.
This is exactly why it was that way in POTCO and here in TLOPO until recently. As I mentioned, I emailed them, they are aware and even pointed out that it was
not a bug before. From all I read in their reply, they plan to revert but are trying to take out a mass of bugs in the sailing loot that were causing issues.