If you select a folder with the functions in the toolbar then you can set on the fly whether subdirectories should be read.
For a permanent setting, use Tools>Options>Folders.
While loading with one of these functions you cannot leave out special folders, yet, only files are read that are supported by MP3tag.
You can filter patterns after loading like
NOT %_directory% HAS .test
Or you use the windows explorer and drag&drop only those folders that you want to load.