dot prefixed files is a kludge that is now a standard rather than an actual hidden attribute like on Windows/NTFS.
The actual heritage is when `ls` was written to exclude .. (dot dot) directories from it's listing the code literally just had the logic to exclude any files which had a dot/period as its first character. Later operators exploited that bug/feature to create items with a dot prefix to make those files and folders hidden. Eventually this became convention.
Whereas systems released more recently understood the need to have a hidden file attribute so made it a first class property.
I do love POSIX and often the first to defend some of Linux or BSDs idiosyncrasies but if there was ever anything that was worth someone saying "I know we've always done it this way but it's shit and it's about time we implemented a proper solution", it would be the dot prefix kludge. (I also know it's easier said than done and would take years for all the tooling to catch up)
The issue is that you have to continue "fixing" lots of individual utilities. In addition to your file manager and `ls`, what about tools like `fd`/`rg`/`ag` (requires adding `snap` to `~/.ignore` or `~/.gitignore`), `fzf` navigation in the terminal (may require updating `FZF_DEFAULT_COMMAND`), "open file" and "save file" dialogs in non-GNOME apps (like Zotero), and so on. The `snap` directory keeps popping up in new places, and discovering all the different ways to hide a non-dot-file is exhausting. In contrast, adding that initial dot to the `snap` directory would avoid the problem entirely.
I have still been using `snap` for the past year, and have mostly been happy with it. It works well for apps like `spotify` and `zotero`, it's a better solution than `ppa` for third-party software, and I like that it tries to introduce a permission model. But not following the dotfile convention is annoying, and not prioritizing a search-and-replace of `~/snap` to e.g. `~/.snap` in the code after four years is strange when this is their most upvoted bug.
This would be nice if it was easy to toggle showing hidden files and hidden files wouldn't show up by default in all folder listings.
Of course you do have system files, which are hidden from all standard folder listings, but aren't usually used by software, presumably because they're too damn difficult to find again (although I really hope google drive realizes at some point that desktop.ini is supposed to be a system file, not merely hidden).