Nothing stops them from doing so.
But I don't think that's the path you'll see super often. Most people enthusiast enough to host their own instance and open it to others probably disagree with ads, and users are very likely going to reject them.
Plus, wether we like it or not, Lemmy is majoritarily used by people with a lot of tech knowledge - the exact same group you'd expect to be running ad blocking software.
But if federated social networks keep growing to the point they could rival a platform like Reddit, for sure some ad supported instances will coexist with user-funded ones.