The current version of Matomo (Piwik) is not affected by this vulnerability. Since version 0.5 (released December 2009), Matomo checks (and sets, if required) the MySQL connection charset to UTF-8.
Matomo users are, however, encouraged to upgrade to the latest versions of Matomo and PHP to take advantage of new features and bug fixes.
Reference: ZF2011-02: Potential SQL Injection Vector When Using PDO_MySql
