When you are opening the database analyzer in the TYPO3 install tool, it always suggests to remove the Aimeos "mshop_*" and "madmin_*" tables.
The reason is that Aimeos uses a much more sophisticated way of creating, updating and migrating its own tables. The TYPO3 mechanism using ext_tables.sql don't know that the tables belong to the Aimeos extension and therefore suggest to delete them.
That's nothing Aimeos can get around without duplicating the whole database creation statements for TYPO3 which would be a source of potential problems. So there's nothing to worry about this as long as you don't follow the suggestion.
Please do not delete any Aimeos tables prefixed with mshop or madmin!