So I managed to get rid of the problem for me. It helped to just disable the rewind feature in the menu! The picture is back to normal and the graphic errors have also disappeared.

After updating the system to version 7.2.2 the N64 games are run normal again. There are no stretched formats, black bars or massiv graphic issues anymore.

@djib Ok it's just crazy. After it worked, I now have the black bars again. I didn't have the Recalbox on for a few days and added a few games today (no N64). After switching it on, when I tried an N64 game for the first time, I had the black bars and some graphic errors again. When starting every game with the standard emulator, a message appears in yellow with "load combiner shaders" and "init noise textures". I tried to fix it again by switching the rewind function on and off, but it doesn't work. I then reset the Recalbox to the factory settings, but that didn't change anything. Reinstalling on a different SD card did not solve the problem either. Whether the games are on external storage or the SD card does not change anything, and a different power supply unit has no effect either. I just change the system language to the default settings, turn off the menu music, hide the pre-installed games and turn off the rewind function. I played around with other settings, but nothing improved. Changing the aspect ratio, activating integer scale or overscan does not solve the problem either.

So I managed to get rid of the problem for me. It helped to just disable the rewind feature in the menu! The picture is back to normal and the graphic errors have also disappeared.

Hello, I'm new to this forum!

I have exactly the same issue with Recalbox 7.2.1 Reloaded on an stock Rasperry Pi 3B (without the +). I was able to run some N64 games quite well on that hardware with 7.1.1 Reloaded.
Even Perfect Dark was reasonable playable.
Now I have this black bar in the lower half of the screen, sometimes larger, sometimes smaller. Mario Kart 64 and Super Mario 64 are running quite smooth, even with this issue. But for example in Perfect Dark and 1080°, (wich was also, not perfect, but playable on the older version) I have massive graphic errors in addition to this black bar in these games too.
I used in 7.1.1 and in 7.2.1 the standard emulator. I'm not sure wat that was in 7.1.1 but in 7.2.1 it's Mupen64Plus GlideN64. The same issue is with the Libretro Mupen64Plus_Next, like djib said.
The others are working better, no black bar and less to none graphic issues, but consistently worse performance.