We (ISP) run our own authoritative name servers. Ideally, I'd have a single hidden ("stealth") master (maybe two, w/ anycast) and all of the public name servers would simply slave from that one. If you run PowerDNS -- which supports MySQL/PostgreSQL backends, among others -- you can keep everything in a local database and use standard tools (or write your own) to manage it.

(If I was pretty much anywhere besides an ISP, I'd definitely be using a provider with a fully-featured API. I use Route 53 now for my personal domains but I manage the zones by hand in the console since the RRs practically never change.)