I have done some investigation as regards how emails are handled for non-logged-in users in Blackbaud NetCommunity (BBNC).
Whether the email address comes from RE originally or some other method (imported list, filled in form on website), the emails are stored in the BBNC database. I have worked out how some of the tables fit together if you want to know more.
When someone gets a "message" (I put it in quotes because that's a technical term used by the BBNC user interface) or a newsletter with a link to an email preferences page (i.e. it contains an email preferences part) then BBNC knows who you are by the URL.
For example, here's the URL
example.com / NetCommunity/Page.aspx?pid=196&srcid=132&srctid=1&erid=117
196 is the page id, as used all over the place.
132 is the id of the message (one message for multiple recipients)
117 is the id of the receipient, i.e. the unique number in the database associated with the recipient's email address
That page has a list of our newsletters, a checkbox saying "Check this box to indicate that you do not wish to receive future email communications from us" and a box to fill in your email address.
If the person is subscribed to newsletters then they are ticked. I don't know why it asks you for your email even though it knows your address from the id in the URL.
Looking at the database things change when the newsletter subscriptions are ticked and unticked. If a user has been sent an email because they are a constituent then the "no more email" tickbox I mention results in a profile change through the RE plugin, and when you process it, ticks the "requests no email" box on their constituent record.
If you email to someone who isn't a constituent, and they unsubscribe from all mailings then it stores this information in the database.
Sometimes, and I haven't worked out when, the user email preferences page doesn't have a newsletter list, but just the checkbox and email address box.
If you have problems with people unsubscribing there are a couple of knowledge base articles, BB470402, BB432116, but they just say "create a case". With all these email addresses flying around I'm not surprised things can get messy, particularly if you have the same email address in BBNC multiple times.