Would Have Ate or Eaten?

The Present Perfect tense uses the auxiliary verb 'have' + the past participle of the main verb. The past participle of the main verb 'eat' is eaten', not 'ate'.

Would have eaten meaning?

If you want it to mean: I thought you would have completed eating before we arrived, you should use already, and to make the meaning even clearer, by the time or before instead of when: I thought you would have already eaten by the time we arrived. (This is the one I would use.)

Were eaten or have eaten?

You want to use the past perfect tense (had eaten) when a past action occurs before (or leads up to) another past action. Therefore, #1 is correct. It means you ate chocolate in the past, but you ate it before you ate dinner (also in the past).