I never thought that these three little words could carry that much innuendo, but "Are you happy?" turns out to be one of the most revealing and difficult questions you can ask a scientist. I have encountered it in so many scenarios and it can provide a lot of information independently of the answer.
Let's look at some examples.
The genuine question: How are you doing? Say you are hanging at a social at a conference and a senior faculty you know well asks the question. Depending on how much you trust them you can tell the truth, half the truth, or lie, but this could be your chance to discuss issues you are having and get some mentoring and advice. If someone is truly interested in your well-being, you should take advantage of it, because at this day and age, we need all the help we can get to figure out academia, the job market, the funding agencies and just how to live life in the "post-truth" era...
The hidden question: Are you interested in moving? At the aforementioned social you bump into a faculty member whom you know marginally well or not at all. If they are looking for new faculty and are interested in what you do "Are you happy?" is the easiest way to gauge whether you would be moveable. Anything less than a resounding "I really am. I love it there." will give them a hint that there could be trouble in paradise. Of course the right answer is "Eh, I guess so", as "I hate that horrible place. Please get me out!" may not be the right strategy to find another university. Or to negotiate a killer start-up package.
The trick question: Say that you're okay! This happens when a senior faculty asks you the question in front of another senior faculty at your institution. At which point your brain is racing at a million miles an hour to regain composure and instead of glaring at them "Why are you putting me in this position?!", you quickly say yes and divert attention to how abysmal NIH funding is right now.
The probing question: Am I going to be happy? Very few people ask this all important question at job interviews, but I think it could be critical to figure out what is really going on at an institution. During interviews, the faculty you meet is in "recruitment mode" and has to show the best possible side of their university. The unhappy people are temporarily hidden in a closet. The people you will meet agreed to recruit and sometimes they couldn't say no, but if they are not happy, they have been hiding it. It will take a very skilled actor to crack a wide smile and answer "I love it here", if they are lying. Of course, you must take answers with a grain of salt. Some people are never happy, no matter where they are and recognizing the Debbie Downers may be difficult. But if someone changes the topic "I really like the city" and has nothing good to say, there may be a problem. If multiple people hesitate before answering, there may be a problem. And in some cases, people who are moderately happy may volunteer some of the issues they are encountering, which, if you decide to take the job, will prepare you in advance. All universities have some kind of issue, but coming in with some idea of what to expect may help.
Hope this helps to find your happy place...