With emacs 28 everything worked fine. After installing emacs-29 I see the following: for example typing "Meta + w" creates "H-M-w" which is undefined. With emacs-28 I got "M-w runs the command kill-ring-save" when I invoke describe key via "C-h c".
There is no mention of hyper-key anywhere in my emacs setup. Also "xmodmap -pm" shows that I have no hyper-key modifier defined. Also xev shows that keyboard generates a Meta_L event, no mention of hyper either.
I run emacs in GNU/Linux (opensuse 15.4).
What happens here?
I had a very similar problem when going from emacs-27 to emacs-28. I had to add some keymap translations for some Alt combinations like "A-Y". These were bound to some special symbols by emacs-28. For example I added
(define-key key-translation-map (kbd "A-Y") (kbd "A-Y"))
which reads a bit silly but binds A-Y to what you expect it should bind to (without that I get the Yuan currency symbol).
Similary adding
(define-key key-translation-map (kbd "H-M-w") (kbd "M-w"))
restores the expected behaviour for the kill-ring-save binding.
Edit: After some fiddling with xmodmap I have an idea that emacs might get confused by my xmodmap setup during startup.
I added "add Mod3 = Hyper_L" to my Xmodmap (and put Hyper_L on some unused key on my keyboard), and now "M-w" is just "M-w". Here is the output from "xmodmap -pm":
shift Shift_L (0x32), Shift_R (0x3e)
lock
control Control_L (0x25), Control_R (0x69)
mod1 Alt_L (0x40), Alt_R (0x6c)
mod2 Super_L (0x42), Super_L (0xce)
mod3 Hyper_L (0x7f), Hyper_L (0xcf)
mod4 Meta_L (0x85), Meta_R (0x86)
mod5 Mode_switch (0x87)
Without mod3 (i.e. no Hyper_L) as it was originally, emacs translates "M-w" to "H-M-w" and similar. To further test the emacs behaviour I removed the mod1 definition (mod1 empty, no Alt_L and Alt_R, but I left the keycode definitions for those two keysyms), and with that emacs translates "A-y" to "A-s-y", smuggling in a Super key, wherever this comes from. Emacs seems to mix actual keycodes with the modifier bits?
Any idea what magic emacs is pulling here? My xmodmap modifier definitions looks about right, considering the many examples for how to remap/add modifiers like caps lock, super, meta, windows keys etc.
I still do not understand why emacs (since version 28) translates "A-Y" to the Yuan currency symbol (and many other similar mappings).