Yes, but Hanna Barbera is also owned by Warners. Isn't that nice? Corporate synergy in action!
Sorry bubba, but it don't work that way.
As a matter of fact, this question came up before, when DCD did their Superfriends line. They could do any DC character affiliated with the show (sound familiar?), but they didn't have the rights for any characters created by HB (Black Vulcan, Samurai, El Dorado, etc.).
Actually this exact question came up at the Mattel/DC panel at comic con... and the official answer is YES! Mattel CAN make figures based on the Superfriends characters created by Hanna-Barbera. DC Direct couldn't at the time that they produced their 2-packs... but the new deal includes ALL Representations of DC characters appearing in all WB films, Television shows and Comics, past, present and Future!
And since there were appearances by Apache Cheif and the others in both cartoons and comics (superfriends comics in the 70's). The official word from the WB rep on the panel is YES they all qualify.
The Mattel rep then asked if it would be something fans would be interested... thunderous applause ensued.