Disabled languages
Yes, the parameter works even if there are translators; the list of them is kept so that one can ask them info (that's the idea). Babels don't seem very useful, the link to Wikipedia in the header is kept; I don't mind readding some stuff but I think the portal needs to look completely different or the note won't be noticed at all (nobody reads warnings).
I think "disabled" is not too confusing as a parameter, but the note can surely be improved, just edit it; I also had to edit Translatewiki.net languages because the process to enable/disable and export or not languages is unclear; and still is. If a language has never been enabled I doubt there's much useful info in a portal: it should be kept only if it has discussions, terminologies or something else, otherwise deleted as Siebrand suggested. IMHO.
I've edited the template note. Thank you for improving the Translatewiki.net languages page.
Are you going to keep a track of site changes to spot new portals when they are set up, with a view to deleting them as they are set up?