"Are we having fun yet" is what we normally say. I would never say "Have we had fun yet". It doesn't make sense in the context of having fun.

This is a comment about culture, not grammar. "Are we having fun yet?" is actually a famous joke. It's a tag line from the (strange) comic strip character, "Zippy, the Pinhead." I think Zippy is funny--sometimes--but the humor is very subtle and ironic. Many people do not "get" Zippy. http://zippythepinhead.com/Merchant2/graphics/00000001/other/images/arewefun.gif Zippy is the classic character, the "wise fool." "Are we having fun yet?" is a very strange question, because usually you know whether or not you are having fun! I interpret it as an ironic comment on the commercial packaging of experience. For example, when I visit Walt Disney World, it seems to me that the Disney organization is constantly telling me that I am having fun. The bus ride from the airport on "Disney's Magical Express" is just a bus ride, but they tell me it is fun. Zippy asking "Are we having fun yet?" suggests that Zippy, _and others,_ look to an outside authority to tell them what they should be feeling. A Zippy strip I love shows Zippy and Griffy (the strip's author) sitting in a diner in Albany, New York... which is basically just a medium-sized U.S. city like a hundred others, not good, not bad, not especially noteworthy. Griffy asks ZIppy "If you could live anywhere in the world, where would you want to live?" Zippy instantly replies, "Albany." Griffy asks "why Albany?" Zippy replies "Because I'm in Albany!"

It's a matter of semantics, different ways that the language can be spun. To ask "are we having fun yet?" is very direct and speaks of one person engaging another person with an earnest question. By wording it "have we had fun yet?" almost comes off as dry, sarcastic even. Technically, both are correct but where and when you would use one or the other depends on the situation and its context.

Grammatically, the difference between the two sentences is the tense. "Are we having fun yet?" talks about the event that is happening at the certain time when the speaker says this. "Have we had fun yet?" involves the event that has already happened in the past. Hope this helps.