I couldn't get an agent so I finished my non-fiction book and just got a yes from a trade/academic press. Should I now look for an agent or will this upset the publishing company? What's the protocol when you submit without an agent and get accepted?
Publishers don't think agents eat small children for breakfast. Mostly.
They actually champion literary agents for a variety of reasons (mostly self serving ones, but better than being considered scum on the pond of life).
It's very much ok to involve an agent at this stage.
The thing is you're going to have to get your skates on. You don't have a gazillion years to consider the offer. This is when you EMAIL agents with the subject line: "I have an offer and I need an agent".
Academic houses are notorious for buying every right they can get their claws on without any way to exploit it. Can you say: audio, foreign and film rights.
At the very very least, you MUST have the contract offer reviewed by someone who understands the arcane argot of the publishing contract. An agent is fine, a lawyer too.