Darth Vader was using his TIE Advanced X1, a prototype TIE fighter and while it was the only one present at the Battle of Yavin it was not the only one in existence (though Vader’s was also modified beyond the usual prototype). Therefore the Rebel Alliance couldn't know for sure it was Vader, it might've been one of the other prototypes or one the first of the production models.
It's also worth noting Vader’s specific model of TIE fighter probably wasn't common knowledge to most rebel pilots (the people who actually saw his fighter) but rather only to the few that have fought him in combat (and survived, and found out after the fact it was Vader in that fighter) (the chances of a rebel pilot meeting Vader on the field being so slim there's no point in briefing them all about Vader's specific TIE fighter).
There's also a possibility that if rebel command (Mon-Mothma, Leia etc...) were aware of Vader, they might not have told their troops due to morale concerns. After all, I certainly wouldn't expect not to be scared out of my flight pants if I was told I would be fighting the evil space wizard.