When GrandPerspective scans a folder, it will include all files and folders that the user is allowed to access. This includes hidden files and folders (e.g. files whose name start with a dot such as .DS_Store files). However, if you only want to scan in the contents of a single hidden folder, e.g. the .Trash folder in your home directory, this is a bit more complicated, as by default hidden files are not shown in the Scan folder dialog. You can do one of the following to scan a hidden folder:

G
keyboard shortcut in the Scan folder dialog.
This will let you enter the name of the folder to go to, even if it is hidden.
For example, when you are in your home folder, you can enter .Trash to scan the contents of your Trash.