"Sometimes after making my magic folders invisible they still show up in directory listings, even tho I can't access them or their files. Why?"
Many programs keep their directory listings in memory. So if you use the program while your folders are visible then the program will continue to use the old directory information even after you hide your folders. Explorer does this. To make matters even more complicated sometimes programs won't refresh their listings even when told to do so. This is probably because Windows notices nothing has changed in the disk cache so it feeds the same directory information as it did previously.
In some cases you can't even force the program to update it's listings. For example, we did some tests hiding the "Documents" System folder. Sometimes it would accurately reflect whether it was hidden or not, but sometimes it wouldn't. It would show the list of documents when they were hidden (although clicking on the document wouldn't work) and sometimes it wouldn't show the document list even tho it was visible - and we couldn't find any way to force it to update it's listing. We can only hide/un-hide the files. We can't control how programs react to this.