Cicero does this more than once.
In addition to what you found in De oratore, we have
ea ratio atque doctrina
(also in De oratore)
ratio et doctrina praescripserit
(in De natura deorum)
indicating that Cicero does see ratio et doctrina as a single entity.
This appears to be a case of hendiadys, using what is grammatically two entities for what is ...
Esse doesn't take objects, but instead has predicates, and its only job is to link the predicates. The predicates are usually in the nominative, but if they're not, they won't be problematic.
Usually, esse does link two nominatives, like Equus bonus est, "The horse is good", but a genitive can also stand alone in the predicate, like Equus est ...
Technically, the verb esse does not have an object, but has a "predicate" which can be either a noun or an adjective. But you are right in a sense, the predicate does agree with the subject and is in the nominative case.