No, it doesn't necessarily include the sizes of hidden files. I've tried it, before my previous post, that's why I said it. It depends upon how you select them.
Go to the Windows/Winnt folder (as this will have hidden stuff). Set the view to hide files, highlight the first subfolder, go to the end, shift-highlight the last file, so all are now highlighted. The total size you get is the total of the highlighted files. Which excludes an hidden ones.
But if you do ctrl-a, it understands you may be wanting to select all the files, and asks you.
I haven't tried to find out what exactly happens re subfolder sizes and hidden/not, but I just suggested making sure you weren't hiding files, as it might have some effect.