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I simply would like to know what happens during Thunderbird's email compaction. What data is removed or altered to achieve compaction? Are attachments removed?

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Technically, attachment was embedded on email body. It is not stored separately with email header and content. The mail clients only parsing the raw body of the email to looking for attachment and present it to you in nice UI.

In Thunderbird, "Compacting" a folder has nothing to do with compressing or zipping a file. When you delete messages in Thunderbird, they aren't physically deleted. Even emptying the Trash does not get rid of them. Instead they are marked for deletion and hidden from view. They are not physically removed until you "compact" the folder. This is a tradeoff done to improve performance in large folders.

So with two above facts, we know if you already have deleted an email and compacted its folder, then deleted email and its attachment was deleted too.

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