Same thing for me, using Pro 3.1.1. Delete a featureclass with 100 records takes over a minute. Rename also takes a long time.
I did some performance testing on some thing and found that basic operations like arcpy.Exists or arcpy.Describe are 3 to 25 times slower than a similar machine when going against and enterprise GDB (Oracle in my case).
Example results for arcpy.Describe were:
Pro 2.9: 0.1seconds
Pro3.1: 4.02 seconds
I have submitted this to ESRI and it is logged as a bug BUG-000161441
I'm not sure if the cause is the same but it seems to be very widespread. If these basic tasks are so much slower I'm sure the cumulative effects are even worse.