Edit: No need to read this post, I misunderstood the problem
@Martin Bergwerf
I think I found a Way how to select all Zero-Faces.
As their one common thing should be that they have no Volume/Area, creating one and then select Similar Area should do the Trick. (To then delete them and merge Verts by Distance). Apparently “quad” Zero-Faces have a lower Volume/Area than “tri” Zero-Faces though so we need to play with the Threshhold a bit.
Add a Cube/Plane, extrude one Side but rightclick right away so there is no visible Extrusion but Verts laying on top of each other (connected by Zero-Faces).
Then go into Face-Mode + Xray-Mode to select the Zero-Face(s) just created. With the Face selected as Active press Shift + G and select Area. Change the Threshhold to 0.000001. That should select every Zero-Face.
It worked in my Tests but I don’t really have a File which has those natively (afaik) so if someone could varify if that way works, that would be nice. Also see if the not mergable Verts even Merge afterwards. Because if not then it does not make sense to select and delete the Zero-Faces anyway.