I just about never remove the barrels from my long rifles but maybe once a year to once ever 2 years .
If you have a browned barrel , you have a rusted barrel . As long as the barrel was browned properly , you should not build large iron oxide rust be it on the top or in the barrel channel .
Cold Blued barrels are different story and depending on the Bluing used , it may not do anything to resist rust .
If however your out in the rain snow or other wet weather its not a bad idea to check the barrel when your all done to insure that your oil , grease or wax is doing what its supposed to . Once you have insured it has , there is little reason for it not to continue since its locked under the barrel and not subject to wear .
Myself when I finish a barrel , be it browned or blued , I coat it with hot linseed . Thus when the barrel is put in place there is very little worry
On the pins . Take them in and out on the same side . Round and polish the ends and you will have no more issues with pins messing up the holes .
On the subject of bedding either your barrel is bedded or its floating .
Beading the tang does not produce the same purpose as pillar beading does on a center fire. Thus we cant really free float a Traditional muzzle loading side lock barrel .
Add into all that is whats called barrel harmonics . Which is different for muzzleloaders .
But anyway , my point is that unless the barrel is fully bedded , then you have areas where moisture can be trapped. Don’t forget that your stock has to be able to breath to some extent .
So while moisture may not get to the bottom of a fully bedded barrel , it can get under the barrel at the muzzle or along the edge of the fore stock . But again once the barrel has been coated and then checked to insure the chosen coating is working there should be very little to no reason to remove the barrel other to insure ones self .