I don't "regularly" remove my chain to clean because constantly removing pins will weaken the holes and pins that you take out. Do that often enough to one specific pin and it'll pop out on its own. I don't use a quicklink because it's made of different metal than the chain and won't wear out at the same rate as the rest of the chain.

If I ever have to remove a chain I put it in a Gatorade bottle with some kerosene (an active ingredient in most bug and tar removers,) and shake/soak it. Take the chain out and lay it flat side down and blast it with compressed air from the side to remove the leftover grit and kerosene from between the rollers and plates. Then leave it to completely dry. If you clean a chain good enough you'll see that one side of the chain is more worn than the other side. There will be little nics, dents, scrapes and smooth highly polished surfaces on one side while the other side still looks new. Only one side of the chain makes contact with the metal chainring and metal cassette. The damage will also be from debris that gets caught in between the metal surfaces during normal use and also from the act of shifting the chain from one ring or cog to another. The other side of the chain will only have made contact with the soft plastic gears in the rear derailer. When reinstalling the chain I make sure to put the side that looks new in contact with the metal gears to try to manage the wear on the metal gears, not necessarily for the sake of the chain. It's my belief that all the uneven and dented surfaces on the worn side of the chain will hasten the wear and encourage uneven wear on the chainrings and cassette which will cost you more to replace than it will to replace the chain. That's the primary reason I reverse the sides of the chain.

I scrub a lot of metals with either kerosene, degreasers or cleaning solvents. I have yet to damage a part enough to cause it to be unsafe or to even cause any damage at all to any bike part. You will probably damage metal parts if you're scrubbing them with strong acids but why would you use those to clean your bike?

Permeated lube? It can and should be removed and replaced as it gets dirty just like any other lubricant. Chains aren't so complicated that you can't replace any lube that is in contact with any inside or outside surface of a chain. In use any lubrication on a chain will get dirty and filled with grit which will hasten wear like sandpaper as the metal pieces rub against each other. Like Sheldon says the stock lube doesn't last very long at all. The stock lube also isn't as mobile as oil is. When the metal plates rub together and scrape the lube out of place the stock lube won't migrate back into place like oil will because the stock lube is closer in consistency to grease that oil. This is also the reason why I avoid using wax based lubricants on my bicycle in general.