The way tag synonyms are implemented, they're not erased from the database completely once associated with master tags; instead, a synonym is recorded, consolidated into and displayed on the site as if it were the master tag.
However, a question may still contain both the master and the synonym if both tags hadn't been merged before the synonym was created. Apparently, this causes the synonym to show up in the Related Tags section on the sidebar when viewing the master tag.
An example of a tag synonym that was created without merging tags is
If you view either one of these tags, you'll be redirected to http://stackoverflow.com/questions/tagged/cross-browser. Now, notice that browser-compatibility is listed as a related tag with 148 hits:
Clicking that takes you to http://stackoverflow.com/questions/tagged/cross-browser+browser-compatibility, which redirects to http://stackoverflow.com/questions/tagged/cross-browser+cross-browser.
There, you see the exact same set of questions, because they all carry the same master tag cross-browser anyway:
Notice also that the synonym is still listed, and clicking it will continue adding the same tag to the URL recursively, but that's a separate matter (and probably a non-issue).
On top of being redundant, this could potentially be confusing for users who aren't familiar with the concept of a tag synonym.
Since a tag synonym is supposed to mean the exact same thing as its master tag by definition, I don't think the synonym should be listed in the sidebar for its master at all, even if questions are recorded with both the synonym and the master in the database.