Isn't that how file sharing/syncing services have worked since the MegaUpload days?
If I upload the same file to two separate folders it's because I want two separate copies. If I change one of the copies, I don't want it to change the other copy.
If that's what you were doing, you won't get affected by this. This is about files/folders that were "hardlinked", which was difficult to do by accident. I think you had to hold Ctrl while dragging the file into another folder, or something like that. (The key to notice is that they're talking about one file being in multiple directories, not multiple files with identical contents.)
That's precisely the behavior you'll get. You were allowed in the previous implementation to upload a file to one location and then put it in 2 locations, such that you would have changes in either location reflected the same way. This wasn't 'copying' a file, it was multiparenting it.
There's advantages and disadvantages to using either.
Any idea if these hard links can be created with Drive clients on Mac/Win?