Does a HONDA 2006 CRF 250r have to have a dual exhaust or can I just get a single?

It doesn't have a true dual exhaust. The pipe splits at the back of the motor into two canisters and is more of a novelty just to get the "dual" look. There is no performance gain. You can and many people have converted to a single pipe system. Aftermarket pipes do come in both single and dual configurations.