I'm not sure this is a "big problem". It seems closer to the usual growing pains of any project that tries to strike out in a new direction. Wayland does something that Nvidia didn't expect, so the driver doesn't cope with it very well. Boo fucking hoo; try running fglrx ~10 years ago (or running gnome-shell with it ~10 months ago, for that matter).
Maybe it could be Wayland be needing input from nVidia and AMD so that they can make adjustments in their binary drivers and make suggestions to the developers as well. Making Wayland work with all drivers, FOSS and binary should be key and all the players involves should be working towards that goal.
Perhaps the title should be rephrased. I use Intel graphics hardware since it's had pretty good support and performance after 2006. I almost thought I had to be worried.
Maybe when NVIDIA makes their driver compatible with Wayland, they'll see this issue and fix it as well. If they don't, we may simply maintain X11 versions of everything until the situation changes, and allow users with other hardware to use Wayland and cairo-gl. I'm not sure if this problem is going to make maintenance much more difficult, and it seems there are some fairly straightforward solutions.
I think that, once distros start shipping with Wayland support, NVIDIA may change their positon. Their original response about not providing Wayland support could have had similar motivations as other projects that haven't totally embraced it. It's simply not ready- why should any company consider supporting something so long before it's going to be used? Even now it would seem a bit premature.
I don't see how this is a problem for Wayland gtk+. It's problem for buggy nvidia blob. I hope nobody will wait for nvidia to support Wayland. It will be another reason to use AMD (if Catalyst won't have any problems).