They’re not exactly deprecated but you shouldn’t really use them anymore if you have a choice. Helm 2 ran a process (Tiller) in the cluster which created all the resources as the service account it was running as (basically as an admin), with no real support for RBAC/multi-tenancy and ensuring that you should be allowed to deploy the things in a chart that you’re asking to.
So instead of running Tiller all the time like you would normally have, Rancher created a separate custom resource (“Apps”) and ran Tiller as the user who created the app on-demand so that it would have only the permissions that user should. This solves the multi-tenant security problems, but now helm list doesn’t work because Tiller isn’t really there.
Helm 3 eliminates Tiller and does basically the same thing we did with apps, natively. So there is no longer any need for our separate type, except for backwards compatibility. (It was also extended to support Helm 3 charts while still using Apps, for “forward” compatibility). That’s what’s in 2.5 (and will still be in 2.6) as the Cluster Manager “Apps”.
Cluster Explorer is the new/future UI that will eventually replace all of Manager’s functionality. The “Apps & Marketplace” in there is the native Helm 3. You can use the regular Helm CLI to deploy apps and see them in the UI, and vice versa. This is what you want to be using going forward.
Questions.yaml are a Rancher-specific “hint” you can add to the chart which lets the UI generate a form to fill out the values.yaml. They are supported in everything (Helm 2 or 3, Explorer or Manager) with the same syntax (technically Explorer supports some extra things like more complicated conditional expressions).