In this case the error was traced back to the "Sitecore/Templates/System/Layout" folder not having a version, which meant that the entire folder and it's contents never got published to the web database (potentially only the original publish of this folder was available in web). Therefore if an item is missing in the web database but appears in the master database, check that a version exists - and if it doesn't create one and try publishing again.
This then caused the web database to be out of sync and there were problems browsing the site/accessing content editor (when web database is selected).
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