My understanding is that beside the difficulty in manufacturing these guns they had another disadvantage in that once the air supply was depleted (as you say 40 rounds) they had to be pumped up by using a hand pump and require some time to do so to full capacity.

The 50 to 75 yard effective range would have made them not quite as effective as the .69 smoothbore of the time using Buck and Ball ammunition. The fact that after 40 rounds the unit armed with them would have been basically defenceless unless supported by others carrying conventional weapons because while the standard cartridge box carried 40 rounds it was not unusual for soldiers to be carrying an extra 20 rounds.

Then you have the age old problems with the Ordance Departments who were resistance to any changes. The Spencers, Sharps and Henry rifles of the time were far superior weapons. Yet the units that used these weapons usually had to purchase them from private sources on their own.