Dokuwiki will understand the old format. The forward slashes are only for the urls, but internally Dokuwiki still uses the colons. Both this url:
http://www.mysite/wiki/doku.php?id=:namespace:nestednamespace:nestednamespace2
and this url:
http://www.mysite/wiki/doku.php/namespace/nestednamespace/nestednamespace2
will still open this page:
:namespace:nestednamespace:nestednamespace2
Test it out yourself.