IB is a real pain to deal with. It's infectious so will spread through a flock and although some birds will seem all fine and normal they might be carriers and can display symptoms when they are run down etc. If you pop down to the coop at night while they are asleep you will hear the breathing rattle. It can be quite upsetting. I had a bird with it and tried multiple things including tylan , smoke bombs, and all sorts of breath easy potions but I lost her in the end
That said if your birds do have fowl pox that could certainly contribute to the condition of the shell.
I would have a listen while they sleep, see if they gasp at all or sneeze and whether they have runny eyes. They won't necessarily have all these things. My little hen didn't gasp till the end and her eyes were fine but at night she sounded like she smoked 60 a day and she sneezed now and then each day..
Hope it's not IB and just the fowl pox making them poorly ...