If your snake is hanging out in the water bowl it is doing so for one of three reasons:
Temperatures are to high
It has external parasites; most likely mites
It is about to shed
"Scale rot" or dermatitis can usually be traced to burns, bite wounds, retained skins, tumors, parasites, soaked substrates, or filthy cages. These conditions can expose the snake to bacteria as well which can lead to abscesses, stomatitis, pneumonia, cellulitus, septicemia, and potentially death.
You can treat the "scale rot" by placing the snake in a tub with paper towels soaked with betadine (10% povidone-iodine) for 30-60 minutes daily. Rinse the snake off before returning it to it's enclosure. Then apply neosporin or Silvadine cream to the affected areas if bacteria is suspected or Micatin if fungus is suspected. Use newspaper or paper towels in the enclosure until this is cleared up. Anti-biotic treatment may be necessary in some cases if the infection is severe or the bacteria has spread and other symptoms are present such as evidence of an RI.
To keep humidity levels up in glass aquariums install 6 mil plastic to 2/3's of the lid and duct tape it to the lid. Use cypress mulch as bedding when all ailments have been cleared up. Gently misting the enclosure (NOT the animal) once daily may be necessary in some scenarios. To ensure adequate ventilation you can use an aquarium air pump. Run a piece of aquarium tubing into the enclosure and attach it to the air pump. This is old school but it works.
The issues you are having go back to lack of research. These are husbandry related issues. I really don't mean to harp on you but it is what it is. If your vet is saying your husbandry is good and you are still having these problems then you need to find a new vet. You also need to read some books on ball pythons (there are many out there) and reptile husbandry. Care sheets and pet store employees are not the best sources of information. Care sheets are designed to give you the very basics until you can do more research on your charges. The fact that many books have been written on ball pythons alone should be evidence that a care sheet alone can not cover all you need to know. The internet is full of mis-leading information as well. Anyone can claim to be an expert online and they don't have to prove it. Authors generally do have to prove experience and qualifications.
You need to stop feeling sad and sorry for yourself and start doing more to correct the problems. You are not the one who is suffering, your pets are due to lack of good husbandry. Now quit feeling sorry and go do something about it.