The "Hide Communities" page (on the "Edit profile & Settings" tab of your profile) says that communities you have hidden will not appear in a couple sections of your profile:
Choose which communities will appear in the Communities and Top Network Posts sections of your profile
Hiding a community means other users will not see it in your Communities list and Top Network Posts.
I checked my network profile and I could still see my hidden communities in all of the tabs there (top, accounts, reputation, activity, favorites). I think the "Hide Communities" feature should also apply to your network profile (only for other users - when you visit your own network profile you should still see everything).