Is it OK to just delete the old Tomcat folders after a Tomcat upgrade with Web Viewer 12.1 for Windows?
You can definitely remove those old Tomcat folders, however, if you still have the old one(s) defined in the services panel, you should remove them before deleting the old folder(s).
Open a command prompt as administrator and change into the C:\Program Files\CA\CA_OM_Web_Viewer\apache-tomcat-8.5.4\bin directory, for example, and type service.bat remove
This will remove the service from the services panel. Repeat as needed.