She didn't even disguise her voice!

The play in Shakespeares time would have been performed with all the female parts being played by men, so it wouldn't have been that much of a stretch as it is today.

Because the play is a comedy...it's supposed to be funny that Ganymede sounds like (and acts like and looks like) a female, yet keeps [poorly] pretending to be a young man...

And there is contextual evidence within the play that Orlando, and Oliver, did know she was a female...

I think this production of As You Like It was too dramatic, the elocution of the dialogue vacillated between sounding stilted and overly dramatic, their physical actions were too serious, and that misguided interpretation would cause viewers to perceive the very few witty and ironic components of the production to be flaws instead of intentional wit and irony.