From the dictionary, both pomelo and grapefruit are translated into die Pampelmuse.
Does German differentiate between a pomelo:
and a grapefruit:
How are pomelo and grapefruit being referred to in a German supermarket?
It depends whether you are asking as a biologist, or as a normal person.
The Pampelmuse (C. Maxima) is the fruit by crossing of which oranges (C.sinensis), grapefruit (C paradisi) and pomelo were made. Biologists don't confuse them. But the pomelo is, biologically speaking, just a variety, so the biologist will call it a "Pampelmuse mit einem Erbanteil von Grapefruit". So, yes, the academic differentiates pomelo and grapefruit because pomelos contain more Pampelmuse than grapefruit and are classified as the former.
My aunt (German) differentiates all of them. My mother's aunt only taught me "Pampelmuse". Until 12 years ago, I only used this word and thought it described both Pampelmuse and Grapefruit. I thought "grapefruit" was the English equivalent. Had I known the pomelo existed, I would surely have called it the same. This mistake seems common, because Wikipedia states:
Die Grapefruit (Citrus × aurantium, Syn. C. paradisi)1, selten auch Grapefrucht, Paradiesapfel oder Pampelmuse genannt...
I think that many Germans don't even know the pomelo exists. My educated guess is most people don't differentiate them and the word old, Northern German people know is Pampelmuse
Grapefruit through the ages
My initial feeling was that "grapefruit" had replaced "Pampelmuse" in everyday usage, but such a case could not be made from the ngram data, looking just at these two words. But adding the terminus "Pompelmuse", mentioned in the comments, produces the expected picture. Strictly speaking, even if the graph contains sufficient data -which I cannot assess - additional effort would have to be made to exclude cases where biologists use the terms carefully.
Ignoring the above statistical problems, the following is suggested by the Ngram data:
Regional preferences in speech
The regional distribution of these words is shown in this Linguistic map, conforming that nowadays "Pampelmuse" is a northern German term. An explanation of the map is missing.
Well, I can tell you in Austria (and in the south of Germany – especially Bavaria) we don't use the word Pampelmuse neither for pomelo nor grapefruit. It is more used in the north of Germany.
In a supermarket they are easily referred as grapefruit or pomelo. But anyway, a pomelo is not so common in every supermarket.
I know Pomelo as a way larger fruit that you can pull to pieces. It's very sweet and usually comes from China or Vietnam when it's sold in stores. It has only recently shown up in supermarkets. We call it Pomelo in German, and I don't think many people know it, though it seems to get more common, as supermarket discounter chains like ALDI and LIDL usually carry it.
The Grapefruit has been around way longer. I've known it since I was a kid, which is more or less 25 years ago. It's common as juice, often also called Pink Grapefruit-Saft. You can also buy it in the discounters, where it's usually around 1 Euro per piece. It's very bitter, and you would normally slice it in half and eat it with a spoon or filet it and put it in a fruit salad.
Pampelmuse is a different fruit than Grapefruit and definitely not a Pomelo. Pampelmuse is also known as Citrus maxima. It is the parent that was hybridized with Orange to get the Grapefruit.