Is there no way to let invisible layers act like there were not there? (all objects not registering/blocking clicks)?
I used some invisble layers for UI menus because its easier to just show/hide a layer instead of 30+ objects.
I don't think so. In my case I finally gave up and used a different layout for my menus. After all this is not what layers are for. Still, if you HAVE to use layers for this kind of thing it is a pain in the butt. What I suggest is using control instance variables, like registering clicks only if "isClickable" is true.