What's the best way to ask "how many hours do you work" at an interview at a start-up?

Just ask "how many hours will I be expected to work" or "what is a typical work day".  If you're expected to be on call or work from home they'll need to tell you that, since you might need to be set up for remote access.  I'm terrible at doing anything in the mornings but have no problem working late into the night so I'm always straightforward when starting new jobs about what the expected working hours will be.  You may be able to negotiate that as part of your job offer too.  And remember, it's not the Manhattan Project.  Round the clock work is a sign of a broken process in quality control or expectation setting or allocation of resources.

The best way to handle this is to let the interviewer know, explicitly if necessary, that you're willing to work beyond 9-5 and maybe even add that you won't have a problem working from home in the evenings. If the company expects this of their employees, the person interviewing you will just move along or will acknowledge and agree. If this isn't something that's normally done at the company, he'll make sure to tell you. Example: once I expressed the idea that I didn't consider my day at work to necessarily start at 9 and end at 5, but that when there's more work that needs to be done, I'd work on it until it got done. The hiring manager told me that he personally has a family and tries to leave the office every day at 5 to spend time with them, and that he didn't ask his team members to put in any more time than he did himself. He hired me and was a fantastic boss.