I always remove the nipples (cones as some call em) when cleaning. Do so after shooting unless as some have advised I plan on shooting the next day or two. If I do plan on a next day or two shoot, the cylinder gets sprayed with a little WD40, clean before shooting. If ya don't remove the nipples, the nipple recesses on the back of the cylinder get layered with a crusty residue that is a bearcat to remove with the nipples installed. PITA at times with nipples removed-alot of brushing. Nipple removal I hate, but necessary. Like trimming brass before reloading, despise doing it, but needed at times. Scrub the nipple recess, nipples, twirl pipe cleaners in the nipple hole and q-tips in the interior of each chamber. Always put a dab of anti-seize on each thread.
One time I had the brilliant idea to clean my percussion cylinders after a shoot leaving the nipples on. Soaked the three cylinders in a 2 gallon bucket of fairly warm water. Can't recall if I added dish detergent or Ballistol to the water. Anyway put a pressure tank wand on the hose, picked up a cylinder, held it under the solution, and placed the wand end into each chamber and also the external nipple area and blasted away. Was an excellent blaster of residue and crud. Cleaned very well, BUT-was messy, very messy. The air pressure shot water/suds all over me and surrounding area. I did it on grass as I thought it might shoot solution some, but not to the extent it did. Should had on my yellow slicker. I did turn the pressure tank down after the first cylinder as it was set around 100 psi but the other two were still messy. Only one go-around doing that. Took nipples out anyway as water can creep into the threads I assumed, reoiled each cylinder, added anti-seize. Good cleaning method but went back to original method.
I have had up to five cappers broke down once for cleaning, but they all had their own area to lay so as not to get parts interchanged. Usually keep it at no more than two. Love FF/FFF revolver shooting, but the cleaning is a pain, but needed. Saw a '58 Remington once that was left to lay for a period of time by a guy who liked to shoot but not clean. He gave it to me for TLC, later years after he quit shooting it was real nasty. FWIW I never do a complete revolver breakdown every time I shoot, couple times a year for the receiver parts. Then sometimes I just squirt gun cleaner into the receiver when the grip and trigger guard are removed, then blast it with air. Gets em clean, relube and reassemble. At times I take a needle oiler as long as the action is working (rarely get any cap frags, a tight fit between cap and nipple works wonders) and squirt a little pure Ballistol into the action. The Ballistol does its job of keeping things lubed and any fouling soft. How they did it back in the 'Ol days, not really concerned, do it as I see fit for corrosion free metal, long firearm life, and smooth operation.