Hmm... a trawl of the admin menu has turned up Configuration -> Server Settings -> Database and Paths; this contains an entry for "Forum URL", which is currently set to /forum
There's a warning at the top of this page:
Be very careful with these settings, as they may render the forum dysfunctional.The
SMF online help repeats the warning, and then says of the "Forum URL" setting:
Forum URL - The URL to your forum's directory, without the trailing slash (/). This URL is used throughout SMF - all dynamically generated URLs (except those with their own settings) are based on this setting.
Since I've not managed to find any admin settings related to notification e-mails at all, I suspect that this setting is being used when e-mails are created. However, it's almost certainly being used in a lot of other more significant places too, and I'm very wary of changing it. So we might just be stuck with this until someone at SMF redesigns the software and setting structure to disentangle the URL used for e-mails from the one used internally.