They still drop them in the First Ascent after you've finished the Pharos.
I tried farming the monsters up there when I was starting my run on the Subterra and found the monsters on the First Ascent didn't actually drop any black orbs. Either the game was being stingy (y'know, just out of spite) or the drop rate is affected in some way, I think.

Either way it was substantially easier to just farm the monsters in the Subterra, all of whom have a set drop rate, and it will be better in terms of EXP.