"Did you have dinner last night?" is fine. You're just asking a question for general information. You would use the past perfect ("Had you eaten last night?") if you were trying to contrast it with other events in the past that happened after dinner.

So if I say, ''Did you have eaten last night?'', is the meaning still the same as ''had you eaten last night?'' ..?

"Did you have dinner last night?" would be a better way to phrase that. I could have eaten at any time last night, so if you want to ask about dinner specifically, you should include that in the question. The past perfect tense is also not really appropriate here. Check out this website to review when to use it: http://www.englishpage.com/verbpage/pastperfect.html Hope that helps.