Wont they have a naming/versioning problem?

No. Perl 6 has its own version scheme, and the number at the end of the language name is just a number.

I'm not a particular fan of that - they should have changed the name entirely, IMO, eg. to Rby - but Perl 5 is not getting discontinued.

They have it already. Perl6 is about 10 years old, had at least 4 virtual machines. When it was announced people thought perl 5 was obsolete. And in the same time came RoR. A few years(like 7 maybe?) ago a some new developers took over perl5 and added some really interesting new features. That made some perl6 developers unhappy, wanting to focus community around perl6. Perl5 developers believe a completely new language should have a different name. Some suggested renaming perl5 perl7. Then there was a website perl11.org redirecting visitors to scala-lang.org. That was about 3 years ago. Since then - I don't care:) Perl6 will have to find itself a niche. The one once occupied by perl5 - a ducktape of the web is now taken by js. So, a long transition is better than a remote perspective of unknown transition.