We've never seen that, but it shouldn't be a problem. You have only one set of files and one set of tables in the database. So it's just that HikaShop is registered three times in the extensions installed but you only have it once really.
If that doesn't doesn't break anything, then you can just ignore it.
Otherwise, you would have to edit the joomla template #__extensions via your phpmyadmin and remove the unnecessary entries for HikaShop but I can't guarantee the result so make sure that you do a backup first before doing that.