As far as I know 'Johnnies' are British soldiers (specifically recruited men - much later became 'Tommies'), not sure why American marines would be referred to as such....

As for the 'go down', maybe it's that time honoured tradition in song writing known as "well it sorta fits....". You know, it's a work song, it's a good gutteral sound to heave on, 'go' is an action word which reinforces what you're supposed to be doing once you hit this bit of the song...yadda,yadda,yadda... Or they could just be making it all up as they go along.... *G*