Well, we’ve landed https://github.com/snapcore/snapd/pull/11200 which should open any link, as long as there is a handler for a given scheme on the host side. Sadly it’s in edge channel of snapd only.
Thank you for linking this thread, I will try out couple of things 
I still think it is something with snap, because when Obsidian is installed from aptimage the linking works fine. Maybe the flag -dangerous required to install Obsidian snap may be part of the problem? @mborzecki I am not a snap expert, what does it mean edge channel in this case :)?
If you’re on Ubuntu or Debian, then snap refresh --edge snapd. You may need to log out or better reboot as there’s a user session daemon snap userd invovled, but it’s not clear that the session is completely torn down on logout.
Keep in mind though, the edge channel snapd is a daily rebuild of the current master, so expect it to refresh quite often.