I've noticed that, for users with hidden accounts, it's still possible to see reputation changes on their hidden communities from their network profile, yet it is not possible to see the hidden accounts in the "accounts" section.
Just as an example, I have hidden Arqade from my communities. When I'm logged out and I view my network profile (which you can view for almost any user by literally just clicking "view network profile" below their list of accounts), Arqade doesn't show up in my list of accounts (it should be third by order of reputation):
But I can still see reputation changes on Arqade from the "reputation" tab:
Go ahead and check it out if you wish.