I read somewhere that "the short" could also mean "humble," but there was no evidence to support this, just a claim someone made on the internet. Also he was called Pepin the Younger and I wonder if Short wasn't somehow related to that.
The nickname “short” (under its form parvus, “small” the first to be attested for our Pippin) appeared in the 11th century, apparently in Flanders. However, there was a precedent to this use, though not for the same person: Ademar of Chabannes, who wrote an history of the Franks in the first third of the 11th century, said that Pippin of Herstal (Pippin the Short's grandfather) was brevis. There was an obvious need to give nicknames to the various Pippin of the Carolingian families; Charlemagne's father, great-grandfather (Pippin of Herstal) and great-great-great-grandfather (Pippin of Landen) unconveniently happen to have the same name (not to mention two of his sons).
Therefore, it seems that there was, in the 11th century, a vague understanding that someone called Pippin had been small. Several possible explanations exist; one of them, that you have mentioned, is that a semantic shift occurred from minor (the Young) to parvus. More interesting, in my opinion, is the short opuscule on the life of Pippin and Charlemagne written by the monk Notker of Saint-Gall, in the last years of the 9th century (a long time after Pippin's death). It is in fact a compendium of anecdotes, without obvious historical value in terms of the reconstruction of events. Two of his passages can explain the eventual apparition of the nickname:
One of the tales written down about Pippin tells us that in order to prove his strength to his generals, he fought and killed a lion in an arena. There should be no need of saying that this is obviously false; but relevant to your enquiry is the fact that Pippin is compared to the parvus David and the brevissimus Alexander (the Great!). In both cases (even though the case of Alexander is somewhat less clear), it appears that their nicknames are due to their relative height, in comparison to the giants they faced. Similarly, implies Notker, Pippin was able to defeat enemies apparently much more dangerous than him.
Another tale, about Charlemagne, mentions his eldest (illegitimate) son, Pippin the Hunchback. His disability is well-attested in reasonably early sources—Einhard, the author of the Vita Karoli, describes him as handsome but hunchback. Notker, using Einhard's account (I don't know if he had access to it) or another one, tells us that he was hunchback as well, but adds a remark about him being a dwarf (nanus) (there is no good reason to believe, by the way, that it was true).
From these two accounts, which were then conflated and applied to various Pippins, it is conceivable that the general understanding that I have mentioned earlier on appeared. Additionally, it is not impossible that Pippin was indeed short, and that Notker's first tale was meant to show this feature in a positive light. However, we have absolutely no evidence for this in 8th and 9th century sources. That being said, the people who used for the first time the nickname did intend to say that he was small; but since that they were writing approximately three hundred years after his reign, of course, they are not reliable informants.
/e: the evidence for this post comes from A. J. Stoclet, “Pépin dit « le Bref » : considérations sur son surnom et sa légende” in Revue belge de philologie et d'histoire; the content itself is my own interpretation, or rather my own reworking of the, well, strange structure of the original article.
In a short (sorry) time, we have removed a number of answers which have said, variously, "short" relates to his height, his age, or his habit of speaking little.
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This book claims that the nickname came later, so we aren't sure where it came from. The author says that Charlemagne had a illegitimate dwarf son, so it's even possible that his father could have even been a dwarf. But it looks like we just don't know really. I also see publications online that say it was because of his stature, but I don't see any sources on them. The author is a psychologist and not a historian, but I don't think she would just make up that line.
In contrast, there is this book which claims that it was truly about the stature. However, the book was written two hundred years ago, and I'm more inclined to trust the more recent book by an expert held to modern standards.