If it's within my agency, I'd answer the question because we're all pretty close and depending on the relationship, I might go more into depth than a general "I'm doing pretty well." Unless it's an email that is important/formal and has the potential to be forwarded to others. And the only emails that are sent that are that important are policy emails, but those are single emails not chains.
If it's in a communication to another organization, it depends on the content of the email and my relationship with the sender. For instance, I recently emailed the director of another shelter. The shelter was recently undergoing some major renovations. I asked how she was holding up with all that in the beginning of the email. I just had a quick question about their services. It wasn't super important.
My work is very informal so I can't think of an instance where someone wouldn't just say "I'm well. Thanks for asking" or something like that.