In Thunderbird 52.9.1 on Ubuntu 18.04, I found the oversized emojis annoying because they covered other messages in the inbox (e.g., in Facebook notification mails).
This issue seems to be unsolved currently (see here).
Fortunately, the situation can be mitigated by disabling the Noto Color Emoji font.
- Install the Font Manager tool: sudo apt install font-manager
- Open the Font Manager: font-manager
- Select System in the left panel and search for Noto Color Emoji in the right-hand side search box.
- Deselect the checkbox to the left of the font name.
- Restart Thunderbird. Now, the emojis should be replaced by placeholder glyphs containing digits.
Thanks to this thread for the solution, which I describe here in greater detail.