The rules say:
The original controller of the capital is still in the game but can’t collect income from any territories he or she still controls and can’t buy new units.
It doesn’t mention bonus $. Can bonus $ still be collected?
Calvinhobbesliker is correct.
Whats the ruling on your other NB/AB if you lose your capital. I see you noted can’t repair your own ships (skip that phase), but will your other NB’s still repair your allies ships? Also do you and your allies still get the +1 movement from your other AB & NB, if you have lost your capital.
My thought is that your AB/NB in other tt are still 100% functional as long as they are not damaged (you won’t be able to fix them). They still get +1 as far as movement (for all powers on your side), and can still repair allied ships (yours can’t be repaired as noted above),
Your thought is correct.