Can't open dev menu via CMD+D or reload via CMD+R any longer

Have you tried accessing the Simulators Hardware?

Simulator > Hardware > Keyboard > Connect Hardware Keyboard

From Menu Bar, I/O -> Input -> Send Keyboard Input to Device. It really helps.

This is indeed really annoying. I figured out a solution I haven't seen here yet, and hope it helps anyone. Go to I/O -> Input -> Send Keyboard Input to Device. And you'll see next time you press CMD+D or CMD+R it'll work. However, it somehow resets this every time. To overcome this, simply add a system keyboard shortcut:

Send Keyboard Input to Device => CMD+D

Now every time you press the shortcut, it'll also invoke that command to make sure the shortcut is sent to the app.

See here for how to add system keyboard shortcut if need be.