"Weren't the .38 short and long colts already really .357's?"
Maybe, maybe not.
I've at least one example of a .38 Short Colt in my collection that has a heeled bullet. I also have a .41 Short Colt and a .41 Long Colt, both of which have heeled bullets.
The .38 Long Colt, I don't know if it was ever offered with a heeled bullet, but given the time when it was introduced (around 1877), it's very possible.
Smith & Wesson was, I believe, the first manufacturer to employ non-heeled bullets in their new cartridge designs. The Russians insisted on non-heeled bullets when S&W developed what would become the .44 Russian cartridge in the late 1860s/early 1870s.
This period was one of HUGE transitions in the development of cartridges.
The best way to explain it, though, is that the naming of cartridges in the US has never been an exact science; and has always had a lot of marketing driven considerations attached to it.