Using the nuke in no way lowers the points you earn, just your imagination.
You can get 36k from level 3-3 and there's always the "AFK rubberband second anthill 1-1" method to cap at 65,500. Just got my 1000 last night and I got the game on July 3rd, pretty much played nothing else but a bit of Ms. Splosion Man.
~Alan | Anime
I award you no points, and may God have mercy on your soul.