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Seems to me that it's really up to each resource. I have added a flag in this case to the MySql plugin.
It would be kind of nice if this was made more general, where for every resource you could somehow disable discovery.
Non-top-level-servers or services are auto-imported into inventory. If they later become defunct (i.e. their underlying tables go away), RHQ has no builtin mechanism to automatically uninventory them. That means you'll have to manually univentory table resources once they become defunct, otherwise you'll end up with a whole bunch of DOWN table resources in inventory that correspond to tables that no longer exist.
So I'd say you probably don't want to autodiscover the short-lived tables.
One potential way to tell the plugin which tables are short-lived and which are not would be to add a "excludedTablesRegex" plugin configuration property to the parent resource type (database?). The table discovery component could then exclude any tables whose names match that regex.