Some have said on this forum that wick differences, etc, seem to filter things out of the juice, and so on, and lots of reasons. I have tried carto tanks, clearomizers, Stardusts, Kanger T2, and so on. I believe it is simply the by-products of vaporizing some of the elements in the juice and not others. I notice that to cause juice darkening easily, turn up the heat. Using a VV device, it is no problem to darken the juice by the time I get to the end of a tank. I can pour the remainder out, and even the wick retains enough to begin darkening the new juice! If you watch, the darkening effect begins at the wick.
In an atomizer you can't see the results. Every once in a while, you don't like the taste of your atomizer, so you clean it. Much has been said on these forums about cleaning attys, and it's simply to get rid of the gunk, junk and sludge just as you describe above.
In a cartomizer, it's still not as visible. I have used carto tanks and the same thing happens as in all tank situations. After a while, the sludge becomes evident, juice darkens, carto gets a hard draw.....The carto gets thrown away.
Along come the clearomizer devices, and all of a sudden all is visible. Only difference between these and the other devices is now you can see what is happening. Atomizers are simply a coil of wire around a silica wick in a ceramic cup with a bunch of steel wrapped around everything. Clearomizers are the same thing, minus the steel wrapped around it all. The only difference is with some clearomizers the coil is higher and more near the lips, and the delivery of the juice varies a little more.
In short, anytime you have a tank situation to contain this gunk, juice will darken and change flavor. In a clearomizer type device you can simply see it better. And with the new 1.5-3 ml juice holding sizes, it becomes very apparent to people. My solution to the problem is to simply clean when it becomes necessary. By the time I have run 10 ml of juice through an atomizer, I need to clean it. Through a cartomizer, I need to throw it away. Through a clearomizer, follow the recommendations; some to be thrown away, some to be cleaned, some to screw in a new coil.