how have i never thought more about the industrial design of the IBM 5120, and those *upright* 8-inch floppy drives? 
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horizontal is definitely more common but I don't think there was ever any problem with vertical ones. There's more than a few computers with vertical ones.
I do seem to remember that iomega's Bernoulli box was supposed to be mounted (or the disks stored?) horizontally/vertically only, because of some possible issue with dust settling on the disc? I can't remember the details.
maybe @TubeTimeUS remembers.
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