At the time, "hard disk" referred to the spinning disk inside the computer & so though "floppy" wasn't technically accurate when referring to the 3.5 inch floppy, it was a nomenclature referring its utility or type rather than a physical description actual object itself.
"Floppies" were the things that you stuck in and removed... didn't matter their covering material, nor what size they were.
It's interesting to think about how many of our words have the same kind of history; once having a widespread descriptive meaning associated with physical traits of the object itself which ultimately were divorced from the original meaning over time...
I'm going to hazard a guess that most of our nouns have that kind of history... but the interesting thing here is that this morphing happened so quickly and it's because the object itself changed, not some generational loss of original meaning...