Huh, never realized that was a thing. Do the shortcuts in the menu show the QWERTY key or the Dvorak one? I'm curious how you learn the shortcuts if it still shows the QWERTY keys.
Shortcuts all show the correct letter value. So for Ctrl+T, I'd press what is the K key on a QWERTY keyboard. For Cmd+T, I'd press what is the T key on a QWERTY keyboard.
This can get a little confusing, but most common shortcuts contain the Cmd modifier on a Mac, so it's only really Terminal/iTerm where things are different.
My keyboard is still physically a QWERTY keyboard which makes knowing where Cmd shortcuts are very easy, I can just look. I switched to Dvorak when I was 18, but learnt with a Dvorak keyboard so I didn't learn it well enough and when I got to uni and had to use shared lab machines I couldn't manage and had to switch back. Then just over 3 years ago I had 3 weeks off work so switched at the beginning with no physically different keyboards and learnt it all by position and I'm still using it today. Less hand pain, and I can touch type where before I was proficient but not entirely by touch.