The four necessary tags (discussion, feature-request, bug, support), plus the various moderator-only tags (featured, faq, status-completed et al), are presumably automatically included as tags on every per-site meta and not subject to the "automatic deletion of unused tags" algorithm.
I've noticed that other tags also seem to be given this special treatment. Some of the tags on meta.SFF have 0 questions to their name yet haven't disappeared, such as openid and login. I assume the same is true for often-used tags such as scope and tags.