I can't speak to the quality of actual locksets or recommended any products, but LockPickingLawyer on YouTube has a number of short videos discussing smart locks. My impression is most of them are trash at just being a lock. The ones made by traditional lockset manufacturers probably aren't generally good at being smart, but I've been wrong about major brands' commitment to open standards before.
Assuming you can find a decent lock that talks Z-Wave, I think you're on the right track with Zwave2MQTT and a USB dongle. I'd be squeamish about using a Pi specifically in a mission critical security control system for a couple of reasons (reliability, complexity, WiFi interference), but as long as you have keyed backup, it'll probably be OK.
I'll leave it to others to recommend the locks, but as I mentioned in another post her, most battery operated Z-Wave devices, in my experience, report their battery life. Most of mine seem to go from 100% to 70% to dead in about a day though, so accuracy might be hit & miss.
Maybe just leave one door with an old school keyed lockset as a plan B.
My battery operated Z-Wave sensors all report their battery life. You'd need to dig into the integration docs to know for sure but frankly I'd be surprised if they didn't report it as an entity.