This is not an authoritative answer--which would have to be blimey, I don't have the foggiest--but a barely educated guess.
English shop has a cognate in Low-German Schuppen, "shed", think tool-shed, work-shop; cp. Bude "abode, house, building; (coll.) construction work company". This is homophone with Schuppen "fish schales", originally a rare kind of uncountable pluraletantum, if I read that correctly (thus die Schuppe would be a back formation by analogy). I haven't seen these related by the root, but if I were pressed to find a connection, I'd say that roof, cover is the primary symbolism for building ("under my roof, under my table") and that fish scales are significantly reminiscent of roof-tiles. So, if shop was ever understood as a non-count noun, that must have been a while back, perhaps in an isolated dialect. It's odd at least insofar the modern genus is maskulin, der Schuppen, while -en usually implies die (plural noun) or das (nominalized verb).
Incidentally, Frisian was isolated for a long time, though I wouldn't take that alone as an argument. Rather compare shovel, Ger. Schaufel, also Schippe. Again there's something about the form. Comparing Scheibe, Schicht, Schindel or Schiefer would maybe go a bit too far though.
There's also what looks like a verb schoppen, chiefly in the noun Frühschoppen "early bar opening hours, a drink in the morning", and now it becomes uncertain--if it wasn't before. A Schoppen is a measure of liquid, half a pint, related to Fr. chopin, and eventually related to schöpfen, scoop. The problem is that Schöpfer "creator, god" draws the attention of this word. This in turn may relate to schaffen "to work, succeed, create, scape", -schaft "-scape, -ship, -hood" (Landschaft, Herrschaft, Gemeinshaft, Nachbarschaft ...). There' are Schöffel, Chef, Schaffner, Schäfer, that relate more or less. Geschäft means "business", geschäftig "busy".
There's also shaft, that gives me the peculiar image of a shop-keep opening the window lid (the shop?), proping it up with a shaft; Alternatively pulling the blinders aside (Gardinen is another pluraletantum). Cp. Schaufenster ("shop front", literally "viewing window" or "show window"), Schaubude "fare establishment", Ger. Schotten, Luken, Klüsen (closures in windows or ship-pipe-works), and very significantly Laden "shop", Fenster-Laden "window lid" (those on the outside; another unusual maskulin -en noun); also see En. ladle, Ger. Schub-lade "drawer" (as if a lid that is shoved), laden "to load", and perhaps Umschlagplatz "market?", umschlagen "to flip, to swap", Klappe "lid, that which flips and clips", verklappen "to distribute [waste]", market, probably via Etruscan merx, in my humble opinion related to PIE *mey- "to change". Which Laden was first, and how it relates to shop I can't say, but it looks like a loaded semantic correspondance.
PS: The image of a shop-front propped up like that of any fast food truck came when I searched for scappa--pretty much into the blue--which is Italian and relates to escape, which has an oddly uncertain etymology (to cloak, really?). This reminded me of fire-escape, ancient Anatolian buildings with the entry through the roof, and thus outlets over fire places in all kinds of buildings, thus window. shaft is an after thought.
