That’s a retroarch bug/quirk.
It won’t read shader presets or shaders if the /shaders folder isn’t inside a retroarch folder.
You can create a /retroarch/shaders folder and move your shaders there, then it should work.
A more clean approach is creating archives to install the shaders and overlays in the internal retroarch directory.
Just get your /shaders folder(needs to be named shaders) and zip it to shaders.zip, the same for /overlays to a zip file named overlays.zip. Then rename the extension from .zip to .muxzip.
Then grab your your newly created muxzip archives, move them to the ARCHIVE folder, either on the root of sd1 or sd2, it does not matter which, and then in muOS go to applications>archive manager and install both archives.
Now those shader presets and overlays will be available within the regular retroarch overlays and shaders folders.
More info here on the archive stuff: Manually creating installable archives