It was removed in 4ac7f939, because gtk_accel_map_*() functions don't work with GAction (the generated file was empty), and I didn't find a substitute (it was concomitant with the discussion in #68 (closed)).
Don't know, not all features are necessarily maintained from one version to another. For instance, by removing support for GTK+2 (see f590e923), we lost the "multi-select" feature, which has been requested since then (see #57).
In that case this is something that has to be mentioned in the release notes. Some users may wonder why their customized menu accels have been reset and configuring them has no effect now.
Gedit kept calls to gtk_accel_map_*() in its code, but I really don't know why: I see no way to use the empty generated file ($HOME/.config/gedit/accels in this case). I didn't find either any up to date documentation on that subject, only some opened issues requesting for keybindings customization…
I've also tried again to tinker with this in Mousepad code, but I feel like there is nothing to do in this direction, and I don't know if it's that obvious to put this feature back in place.
So I don't think we should block 0.5 for that, but you're right, this should appear in the release notes.
I didn't think to look at it that way, but in the end GtkAccelMap works with relatively little adaptation, so I think we can continue with that. That's what will break the user's workflow the least I think, and anyway, both solutions won't survive the switch to GTK4, so from a sustainability point of view it's pretty much the same.