Because ISBNs get autolinked by the parser, so if what you typed into VE was an un-linked ISBN it needs to be <nowiki>'d.
However if you press space after typing an ISBN it should auto-link it in VE too.
I have seen nowikied ISBNs in articles created by new users with ve. I very much doubt that this was intentional by the user or the user even knows about nowiki. there seems to be an error in ve.
Please change the behaviour of the Visual Editor to autolinking an ISBN, RFC or PMID by default without any extra key press.
This would match the behaviour of the old wikitext editor and it is the more expected behaviour.
In the old wikitext editor you have to explicit type nowiki to make it unlinked, this should be done her too.