Was this hard-linking only possible when performing an action via the web/app interfaces? Because the wording makes it extremely confusing. Even I thought this was going to affect copies of the same file in multiple places. I don't notice any points in their support doc which tells me otherwise.
I definitely see where your confusion is coming from even if I didn't think of that use case initially. It would definitely be a good idea for them to explicitly call out the difference.
There was a keyboard shortcut Shift+Z to add a file to another location (i.e. create a hard-link). Not sure if it still works. The sidebar also has a list of locations that a file is in. Also there are public APIs and documentation for everything.