Regarding cleanups: I'm using flux CD with kustomize. It tracks resources that it created. If I delete manifest from my repository, flux will delete resources that were created from these manifests. For me that's pretty much the ideal workflow.

Regarding hooks: I don't know. All applications that I've used, implemented migrations internally (it's usually Java with Flyway), so I don't need to think about it. One possible approach could be to use flux CD with Job definition. I think that Flux will re-create Job when it changes. So if you change image tag, it'll re-create Job and it'll trigger Pod execution. But I didn't try this approach, so not sure if that would work for you.