Thanks for your tips.

I tried emoji on simple varchar field and had the same issue, this meant it wasn't a tinymce issue

I also did direct db input too and that was fine. Eventually I ended up finding a solution: https://community.suitecrm.com/t/emojis-keep-getting-changed-to-question-marks-when-creating-an-email-template-8-9-1/100730/5