I think I may have figured this out. I am running a multi-store setup on magento CE v220.127.116.11 and using a Flat Catalog. From what I gather the required SQL to update the category meta tags for a single store in my multi-store setup is as follows:-
UPDATE `catalog_category_flat_store_12` SET `meta_description`=[my_desired_description],`meta_title`=[my_desired_title], `meta_keywords`=[my_desired_keywords] WHERE `level` > 1
In this case `catalog_category_flat_store_12` is the flat category table for the store I am targeting i.e. store id 12.
I hope this is correct and that it may help someone else.