I do think the proposed layout of ~/Snap is better than the existing ~/snap directory, but if I’ve got 50 snaps installed it’s still going to feel a bit unwieldy. If many of those directories are empty (or appear empty), then it’s not going to feel like something the user owns. And that is one of the main complaints about the existing ~/snap directory.
Maybe one solution would be to make creation of the directory opt-in? If I’ve got 50 snaps installed, but the only subdirectories under ~/Snap are for the music app and photo manager then the directory will be much more manageable in a graphical file manager. It’d also mean that don’t need this facility (e.g. a game or a simple command line utility) don’t impose visible complexity on the user.
If the we’re only showing these directories to the user when they have a purpose, then they are more likely to accept it.