My suggestion would be to unseal the module class, make your changes and seal it back up knowing there is a possibility that an upgrade will overwrite the new fields you add. What I'd suggest is having that part of your documentation you hand off to the client, "newsletter customized by adding X fields within the Kentico Email Marketing module". If you unseal it and add your fields, it's not standard practice or best for that matter but it is better than trying to rewrite the whole module or manually add the fields you need/want.
Lastly, I'd really look at the reason to add the additional fields and what business purpose they will serve or if they are just there to help with development purposes. Adding a description field seems a bit overkill, just name your newsletter appropriately. Adding the allow users to subscribe field makes sense although if you don't want users to subscribe, then don't put a subscription form on a page for them to do so.