Yeah, that's probably why there aren't strong tools like RDBMSes. However, that isn't so say that you'd never have to run maintenance to make changes on a RethinkDB system... it doesn't make sense to assume that your data always stays in the same format.
Agreed, it definitely has a schema, so to speak
I'm not sure what people would be doing to solve that problem today. My first thought would be to release software that is compatible to a before and after schema, and then once it is deployed, run a complex ReQL query to rewrite records?
(or if happy with a downtime deployment, skip the first part of that step)