No, your decks and notes will not be changed when you delete the add-on.
You should still subscribe to the decks from the add-on to get future note updates. When you go to the Subscribed Decks menu in the add-on (Anki main window → AnkiHub → Subscribed Decks), it will be empty and this means that you don’t get updates. Please follow the instructions above to re-subscribe to the decks.
Hope this helps!