Took my car in to Honda to be serviced?

They told me they'll call me with the diagnosis of the problems at 3 pm. They called me and told me that they ran into timing issues and asked if it would be alright to keep my car overnight. I said okay after they told me they wouldn't charge me extra to keep it overnight. That they will call me in the morning with the diagnosis.

Would it be overkill if I call and ask for an update?

You can call and ask, but I bet the "timing" issue is that a previous job took longer than expected and they haven't looked at your car yet. So they called to check if they could keep it overnight, and work on it tomorrow. Nice of them not to charge you for storage ;-)

Call them back mid-morning tomorrow and see how they are getting on.