I believe that Scaled Composites (Burt Rutan's shop in the Mojave) has customarily not been purchasing wind tunnel time for some years now. Last time I read a story on their use of CFD, it was running on PC's. Before you laugh, recall that the most ordinary of modern PC's exceeds in computation power the "supercomputers" available to design ALL of the nuclear weapons currently deployed by the USA!
Not to say even they did not see the need for some physical testing once: in resolving an issue that turned up on SpaceShipOne, they famously attached a test shape to the Ford F250 pickup truck of a member of staff, and ran it down a runway to collect the data they felt they need to make/confirm the needed adjustment. They themselves describe the issue as flow separation inadequately modeled by their CFD.
For a brief account from Scaled, see
this web page