Both are equally the same--in spoken North American English. The main verb only makes them seem different.
1. Did you have lunch yet? <main verb>
2. Did your teacher come yet? <main verb>Adverbial yet co-occurs with HAVE, specifically, perfect HAVE -ed/-en, which makes the first example appear comparatively more acceptable than the second example--but it's not. The first one seems more acceptable because it houses a verb that looks like a perfect verb form.
In short, 1. houses what looks like a perfect verb form, have, and so makes it appear more acceptable than 2., which houses a non-HAVE verb, come.