http://www.halfapp.co uses the 💯 emoji.
In Safari on macOS I see a question mark in a square. See screen.
I also have this issue in emoji used on my Instagram profile.
Also, in the web inspector, I see the emoji.
And if I use Look Up, the emoji is shown.
Logging in as a guest user I see the emoji.
No duplicate fonts, no fonts with errors.
Apple Color Emoji is where it should be.
And the emoji is displaying just fine in this post!
Permissions have been repaired and re-checked, but I can check something specific if that would help.
If I remove "-apple-system" from the CSS font definition the emoji appear (and of course the font changes).
macOS 10.13, Safari 11.0 (13604.1.38.1.6)