I'm going to have to guess that CFD simulation above mach 1 that is good is probably not something that is publicly available but from reading RUAG's website they use open source software[1]. From my experience with CFD in F1 the main issue you have with CFD is correlation but maybe driving a car around a track is harder to simulate than going really fast in "clean" air.
This reason is what leads me to think that it is a major issue and is why both China and the United States started going into mach 5+ with autonomous craft to gather data for correlation.
[1]: https://aerodynamics.ruag.com/en/aerodynamics/simulation-ana...