Unfortunately, Apple seems to have messed up assistive apps like Keyboard Maestro in Mojave and if you depend on macros, that’s a very bad thing indeed. I upgraded to Mojave late last week (even though it is still not theoretically a GM) and found that although some actions still worked without problem like app launching others (specifically my universal Emacs key equivalents for arrow moves) did not.

I found this thread about the issue on a Keyboard Maestro forum. The hints on that thread helped me work out this solution to the Mojave problem. Note that you may have to repeat steps after rebooting your Mac.

1. Copy /Applications/Keyboard\ Maestro.app/Contents/MacOS/Keyboard Maestro Engine.app to /Applications.
2. In Terminal, kill the Keyboard Maestro and Engine processes.
3. Open System Preferences > Security and Privacy > Accessibility. Grant privileges to both apps: Maestro and the copied Engine. (I also granted privileges to Finder and Safari, which probably wasn’t necessary.)
4. Launch the Engine from /Applications. Check the process list for /Applications/Keyboard Maestro Engine.app/Contents/MacOS/Keyboard Maestro Engine and test your macros. You may have many types of macros and you’ll want to hit as many bits of the OS as possible when ensuring that each kind of macro is properly launched and executed.