I just got the same weird problem, I'm still on 10.12.6 though.
Are your short-command cmd-n working (for example opening up a new window in safari)?
Same problem for me with cmd-m for minimizing windows...
I tried same thing as you and haven't got any luck. Also tried some other things like starting up the Mac in Safe Mode (holding down shift when you hear the boot-sound after turning the computer off and then on)
Try if copy/paste works in Safe Mode, didn't work for me..
Copy something (by right-clicking and then copy)
Then go to finder, and then go to Finders menu bar (at the top of screen) - Edit - Show Clipboard
If there's something there I guess something is working at least.
Not sure how to fix this...
** (very strange) Update: **
So, I went to system preferences - keyboard - special key (I think that's the name in English for that button, the button is just above the 'setup bluetooth keyboard' button).
When I change alt key to work as cmd, it works perfectly!
I am so curious about this, it feels that cmd button doesn't understand its purpose when it comes to cmd-c, cmd-v, cmd-m, cmd-n and so on 😁
I will update to the newest software and see if that helps me out.