Darker colors hide dirt and grease stains better. (I tend to get things dirty easily, which is why I opted for red Ortliebs rather than the bright yellow.) From an aesthetic standpoint, they are less likely to stick out like a sore thumb from your frame. The thought of, say, a "Blue Velvet" Surly LHT paired with bright yellow or day-glo green panniers and accented with with a blazing orange tent stuff sack makes me cringe. At that point, you might as well go for broke and put on bubble gum pink bar tape.
I am with Staephj1. Theft is not something I worry much about on tour.