There are indeed some. Some fanfictions might center around their training sessions together. For example, they could be in a situation where Kakashi is teaching Sasuke a new and difficult ninja technique. This type of fanfiction builds on their relationship in a more action - and growth - oriented way rather than including inappropriate concepts.
Sure. You can also find ones that are set in alternate universes where they have different roles but still maintain a positive, non - inappropriate relationship. For instance, they could be in a world where they are both on a mission to save the ninja world from a new threat, and their bond is more about mutual respect and working towards a common goal.