I thought about just adding an option to control the ammunition amount in the settings. To my surprise, I already implemented this, but I left the setting on hidden.
Now there is a setting in the main menu that you can adjust to your needs. You can also use a power switch and a chest to do more advanced stuff.
It seems to use the ammunition better if it has less. Or maybe combine one nuclear shot combined with multiple normal (and multiple Big Berthas) to clear off the remaining nests.
I hope I was able to help you. Have a nice day :)