It is usually not a problem at export (could be though in complex nestings), but if you want to clean up your .glyphs file, I just added a Delete duplicate paths script to my repository, look in the Paths subfolder: https://github.com/mekkablue/Glyphs-Scripts
My main concern about duplicate paths dates to Type 1 font days. A duplicate path directly on top of another could basically “zero out” the character, i.e. all that displayed during use would be an outline, a very thin one. I recall finding that on one Adobe font. That may not be an issue with Opentype fonts though.
I’m sure I would have caught such a problem during testing, but one never knows.
The Remove Overlap function (Glyphs uses the one provided by the AFDKO) has been much improved. I also remember weird results in a, cough cough, different font editor, back in the good old days.
But sure, stacked paths can confuse the Correct Path Direction function, and they can be a nuisance during editing. Thanks for the script idea, I credited you in the update description.