If you create a new message in Swapnote, and then run Netpass your message will be "sent" to random people. You won't know that they get it, but they will. I have more than one 3DS and I managed to get the message from one 3DS to the other via Netpass, several weeks after I sent it.
Essentially your message, along with any other messages are stored on the Netpass server and it "matches" with other people who use Netpass. When you (or they) run Netpass and you download the data, it includes a random number of other people's Swapnote messages.
Essentially the CECD file on your 3DS is updated with data from the Netpass server. The 3DS in this case can't stop the file from being updated and just accepts / loads any messages provided to it.
If you have Swapnote on your 3DS, I don't think you can do anything to block these messages. You'd have to remove Swapnote (via FBI) to stop getting the messages. And no, you don't seem to be able to block individual people, as the messages come through effectively anonymously (as far as I can tell).