If I am sending a signed mail to an end user, whose mailserver doesn't support S/MIME, what would happen to the message?
Servers traditionally aren't supposed to look inside the content of a message (well nowadays they do often filter for viruses).
The S/MIME stuff only is in the headers and body of the message, not in the envelope. It's for use by the client MUA run by the recipient user, not by their server. So unless a filtering server thinks it's a virus or something, it should just get delivered to the recipient's mailbox, just like any other message.