I'm here now because I was noticing the same thing. I just went to test, in Responsive Design Mode, a website I'm currently developing. The shortcut I used to use for that now refreshes the page.
I think the reason behind the removal of the shortcut from Responsive Design Mode is that Command-Option-R is now the shortcut for "Reload Page from Origin," for some reason. Click on Safari's "View" menu, at the top of the screen, then hold down Cmd-Opt-R and watch "Reload Page" become "Reload Page from Origin." The shortcut for that used to be Shift-R, which I had been using for years. Pressing Shift-R, in Safari, doesn't seem to do anything at all, at the moment, so I'm unclear if this change was intentional or a mistake. It seems like they could safely revert to what it was before... *shrug*.
Not a huge deal, since you can still get to Responsive Design Mode from the menu, or create another shortcut, yourself, as mentioned, but still a bit of a "Huh?" moment.