Did you already have the chance to verify this? I can clearly see that applied tags are not included in the metadata.properties.xml files.
However I did notice that the mysite.metadata.properties.xml which has been created by the exporter at the root level of the exported site does have some sort of summary of the used tags within the site:
The numbers in the tag list are in fact the correct count on how often they have been assigned to documents.
That looks weird to me, because on the one hand the exporter does take the tags into consideration but does not assign them to the actual documents. Do you know the idea behind that?
I thought that tags might get saved to another aditional xml file instead of the per document metadata.properties.xml but grep didn't find any of my tags.
Regarding the thread Bulk upload and tagging that you have linked: The situation described there is different from mine: I don't need to import files from an external third party source. I'm using the Alfresco bulk-export tool and the bulk-import tool which works together pretty well. It is just that the tags are missing for whatever reason.
I don't see creating a Alfresco Web-Script as a good approach for exporting and importing here, since with the bulk-export/-import tools there is a solution provided specifically for this case.
Instead it would be the better option to extend the existing tools to support tags.