I can't seem to get progress for the bounties "Scorn" or "Weapon of Choice" during the boss fights (Both the Fanatic and The Vengeful Hand) during The Hollowed Lair, however, they progress fine during the rest of the strike. I haven't tested if this is an issue in other strikes as well. Seems like it could be a bug, or is this intentional to prevent people from farming bounties in boss rooms? I'm playing on PC, and was doing the normal version of the strike through the director.
This is intentional. Both those fights have a lot of enemies and Bungie changed it some time back so you can't farm the enemies there. If you are searching for a place where you can kill a lot of Scorn, I'd recommend the Bay of Drowned Wishes, the Lost Sector right at the spawn point in the Dreaming City. You can easily complete the 50 scorn Kills there.