Adding my two cents here, I'm a Mac Pro Early 2009 user and I always have this issue on any macOS version newer than 10.14.3 specifically. macOS Mojave 10.14.3 works just fine and I don't have any audio issues there! So, I recommend each Mac Pro Early 2009 user to stay on macOS Mojave 10.14.3. If you're concerned about security, and the apps you use are available on Windows or Linux, I recommend switching to those OS's for more security as Apple has stopped providing updates to the Early 2009 Mac Pro for quite a while. Lastly, if you don't care about audio and just want the latest version of macOS for Xcode or anything that doesn't involve audio, go ahead and install Big Sur! Audio will still be there but it does get unbearably stuttery and distorted once in a while.