Page 11 of the Rulebook: “You must collect income if you can, but all other parts of the turn sequence are voluntary.”
Bonus income from NOs is income, so it must also be collected.
Let’s say there is a German sub in SZ6, along w/a German cruiser. And I want to attack SZ6 w/a British battleship, bomber and 1 FTR. Can the German sub submerse before the British battleship gets a chance to fire on it if the German player so choses?
Yes, before any of the UK units fire.
Also note that your british fighters dont get to shoot at the german sub at all, as you are not bringing a destroyer along with you.