AppData, at least, is only Hidden (not System), so if it's hidden in the main file display it will be because of the folder format.
If you go to Tools -> Folder Options and then click on the Filters tab, is H ticked in the Hide Filter? If so you need to update your folder formats to remove that filter. (See the Folder Formats FAQ if you have trouble making the change 'stick' so it's applied to all folders and new windows.)
For the folder tree, turn on Preferences - Listers - Folder Tree: Show in Folder Tree: Hidden folders.