If the snake is really that close to a shed, it could be just the old, brittle skin being damaged by the roughness of the bark underneath it. After the shed, I imagine the belly will look clean and pristine again. Same if it IS the early stages of scale rot. Very likely it will shed off and the snake will be just fine.

As for spot cleaning the mulch....the difficulty with that is you can't always know when/where to clean and you can't always get it all. Poop is easy, but pee can seep down beneath the mulch and be more difficult to both notice, and to completely clean up. Over time, it can build up into an unhealthy mess. You still need to do complete substrate changes and cage cleanings from time to time. How often depends on how often your snake pees. If I had a substrate like that, I'd probably do a complete substrate change every 4-6 spot-cleanings.