The suppressor or silencer was developed around the same time as they were for the internal combustion engine, and there are three main reasons why they were seldom or never used by the few diehards who still used muzzle loaders at that time. Neither is impossible to work with but both are still a nuisance.
One is the fouling, which can now be minimised by the use of black powder substitutes or one of the few muzzle loaders designed to cope with smokeless. Otherwise it would need to be removed and washed out with water. Still, so does the gun, and how many shots a day do you need on deer?
Much the same applies to the obstructive of any patch, wad or sabot used. Substantial sabots in particular might jam sideways and damage the baffles. A grooved and lubed bullet would probably be best but see below.
The final difficulty would be in loading. Possibly the suppressor would have to be removed every time. but again, in hunting you don't often have to reload a muzzle-loader quickly. Any elongated bullet passed down through a suppressor, unless it is groove diameter and relies totally on upsetting on the first impact of gases, is liable to end up misaligned. It doesn't matter which way up a round ball reaches the muzzle, but for patching, see above. I don't suppose a suitably sized unpatched ball, driven into the rifling, is out of the question, since it works in breech-loading smooth and rifled shotguns. Another possibility to help alignment would be a steel or brass tube, thin enough to fit between bullet and baffles.