The length of your work is put into the description of your book automatically (page count or word count). If you do not think that's sufficient you can mention it in your explicit description you provide for your book. Besides that there may be categories for short fiction, so if you choose one of these the customer can find out what he is buying.
That said, I can understand you want to put it on the cover. If you (will) have several books, some shorts, some full length novels and readers are searching for your name, they maybe won't be aware of the category, but expect a novel if they read a novel before. Buying "just" a short story could be disappointing. But they can get their money back if they want, so even that shouldn't be such a big deal.
If you feel better, put "short story" in a small font on your cover. Not too dominant, it does not need to be readable on the small cover icon.
But this is nothing that will hurt or increase your sale dramatically.