This shouldn't be difficult to do for v3. Would you want non-visible categories to still be accessible? That is, should an invisible category still be available - just not linked anywhere?
Yes, plugins and current (i.e. v2) templates will continue to work with v3 products. However, there may be some cases where we have to remove, replace, or change plugin hooks - if this happens, we'll clearly explain what has changed and what needs to be done for the new system.
Gossamer Threads Development Team
