It doesn't indicate the fort's "difficulty".
It doesn't indicate how many waves are left.
It doesn't indicate other ships in the area.
It. Doesn't. Indicate. ANYTHING!
(At least, not anything you can't glean from looking at the sky)
Skull clouds (like most clouds) gain a pink/reddish hue during sunrise & sunset. This coloring carries over to the eyes of the skull as well, making them appear yellow (when dealing with lights, Red + Green = Yellow), or even red.
