Ondřej,
JFBConnect definitely is able to create UTF-8 usernames and names in the Joomla database. More than 25% of our users have names with some non-Latin characters, and it works just fine. JFBConnect doesn't store the user's name or username directly, we rely on Joomla to do that. If your Joomla User (jos_users) table or the whole database is not configured properly (UTF-8 collation and character set), the name may be translated to the closest characters for whatever your database is setup for.
Hope that explains. There are thousands of international websites that use JFBConnect, and this isn't a problem on other sites, so I really don't think it's a JFBC issue.
Thanks,
Alex