I was wondering is there a limit of amount of skins you can create, and what would you recommend to do in this situation.

There is no limit to the amount of skins. If you want to create a very large number of skins, you may want to consider creating skins at runtime:
Runtime Skins - Spine Runtimes Guide: Customization

The Spine file gets a bit messy looking, because it has some bones assigned to specific skins (if they have different features like capes, hair, etc.). And all of those bones are visible on the tree at all times, even though they are not used in that specific skin. I hope you can understand where I`m getting at

You can use Skin bones. A bone can be added to one or more skins so the bone is active only when the skin it is in is active. This allows a skeleton to have bones that are only used for certain skins. Bones that are not active do not affect runtime performance. Please see the Spine User Guide for more information:
Skins - Spine User Guide: Skin bones