That's Mitch's hackery right there.
Go open SpineEditorUtilities.cs
There should be a #region labeled "Hierarchy Icons" or something.
The way Mitch did it is pretty messy, and it slows down the editor if you have a crapton of GameObjects in your open scenes. This is why you can disable the icons under Edit>Preferences>Spine
I don't know a better way though.
Also, I don't see it happening on my Unity editor.
Do you have extra plugins or windows in or around the hierarchy panel?