It's almost certainly done by non-employees now, through contracting arrangements. While it's possible the unfiltered stream never leaves Twitter's premises or Twitter's computers, and the individual contractors sign an agreement directly with Twitter, it's only one step removed from just sending your stream to the service and getting back an annotation.
Yes, they have contacts/agreements with the parties that get access. Whether that's full time employees or contractors, I don't think that changes the main issue. They will never expose that information to the public.
