Is anyone having issues with .BAK files
They are cluttering the work flow.
No issue here. But, may I suggest that you limit the number of .bak files to be saved. This setting is in the Cubase preferences. I have mine set to 5.
Regards
Here is a workaround which will hide all of your .bak files except ones newly created during your session that day.
https://www.steinberg.net/forums/viewtopic.php?f=285&t=171924&start=25#p921587