After installation of Ubuntu 18.04 (Gnome Shell) I see the same problem with huge icons in Thunderbird.
As already mentioned I don’t have this problem on Ubuntu 17.10 (Gnome Shell / KDE). So it looks like it has something to do with a change in Ubuntu 18.04 base in combination with Thunderbird 52.6.0…
I am on 18.04 and no longer have the problem, I suggest that you try playing around with Mate Tweak and disable compositing as I still think it is theme related!. 
@wolfman, thanks for helping to solve this problem. Unfortunately disabling compositing ( MATE Tweak -> Windows -> Window manager -> Marco (No compsitor)) did not help. Also tried different themes again, without any improvement.
But I will not give up trying other settings! 
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@ouroumov: Here are two sample .eml files. I hope you can use them and hopefully track the problem.
https://send.firefox.com/download/b65172862d/#0PT9pEpaAlAHQXpWuhb_HA
https://send.firefox.com/download/de0e823cff/#vjPPiXm6W4UVPwxYd1uu_w
Confirmed in TB here with exactly the same setup, patched to tonight.
An easy reproducible way to demonstrate this is to subscribe to the Noticing newsletter (which is worth doing in any case). The newsletter contains an emoji in the subject line which displays at about 20 times the size it should be.
Interestingly, I have come across this issue in a couple of Android apps as well …
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I found a workaround by removing the fonts-noto-color-emoji
(apt remove --purge fonts-noto-color-emoji)
But this is not ideal because some emoji are now displayed as a kind of ‘not displayable’ character.
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@Wimpy please take a look at this when you have the time, I don’t know where this is coming from. :x
Please can someone file a bug for this on Launchpad as affecting thunderbird, firefox and fonts-noto-color-emoji and post a link here.
Those of you affected please the mark that bugs as “affects me”.
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I think that this bug is already reported now for U18.04.
Bug #1759286 (and Bug #1761844 is probably a duplicate)
Bug #1759286 gives as a solution to install Thunderbird 57.0b2 from Thunderbird PPA.
I have not yet tested it.
I have tested it. The problem is solved with TB 57.0b2. The icons are displayed in the right size.
(first reinstalled fonts-noto-color-emoji)
sudo add-apt-repository ppa:mozillateam/thunderbird-next
sudo apt-get update
sudo apt-get upgrade
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Although TB 57.0b2 fixes the emoji problem it breaks the time/date formatting and the lightning plugin is not (yet?) supported.
There is also the probably related Firefox desktop icon bug: https://bugs.launchpad.net/ubuntu/+source/firefox/+bug/1760144
Sorry to bump this thread, but something that worked for me was creating a “fonts” subfolder in Thunderbirds’ own folder and placing EmojiOneMozilla.ttf in that folder.
First, download the font itself.
Second, create a “fonts” folder (you need root access for that):
sudo mkdir /usr/lib/thunderbird/fonts
Finally, place the font file in that folder (mine was saved in ~/Downloads, yours may be in some other place, so change the next line, if needed):
sudo cp ~/Downloads/EmojiOneMozilla.ttf /usr/lib/thunderbird/fonts/
Restart Thunderbird and it’s done. Hope it helps!
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An even easier fix:
sudo apt-get install fonts-symbola
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Thanks TuXFrk, (sudo apt-get install fonts-symbola) worked a treat in Lubuntu also.
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@MrRollton fix worked almost flawlessly apart from 1 (??) icon that still showed huge:
Applied the fix provided by @TuXFrk. Now even that icon is normal sized.
Kudos to both for providing these excellent solutions!!
Have just had to re-install because of hardware problems and have the same problem as RHHOEK in three of six e-mail accounts. When these enormous symbols (crowns and party balloons) appeared I thought that it had to do with the royal wedding!
It looks like a Thunderbird problem.
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Thank you TuXFrk
sudo apt-get install fonts-symbola worked for me too
Cheers!