Über dieses Add-on
It is possible to control which folders it will apply the filters to, with a simple inheritance scheme accessible through a new tab in the folder properties.
It is also possible to manually initiate a run of your mail filters across all your folders (respecting the configuration you have made which might stop them being applied to certain folders).
UPDATE: It turns out that there's already functionality to do filtering on sub
folders in Thunderbird, it's just not well documented. It can be enabled by setting the preference "mail.server.default.applyIncomingFilters" to true, or can be applied per folder by setting the "applyIncomingFilters" property to a folder. FilterQuilla (https://addons.mozilla.org/en-us/thunderbird/addon/filtaquilla/) is reported to be able to set that property, although I haven't tested it.
As such, I don't see any need to develop this extension any further; this is it kiddies.