My hair's dark brown, yet in the sunlight or on some photographs it appears to have auburn highlights I doubt Moz dyes his hairs, and in those pics when he was younger where his his hair has reddish tones, he may well have had highlights but dark hair looks like that in some lights.
I was going to say this - yes, in 1999-2000 he had very long hair (for Morrissey standards, anyway) and it was quite dark, especially on top, but you could tell as the tour went on he had a few grays up there. It wasn't even kept very short on the sides and back, as is his norm. It was just quite thick all around. It looked good, but I think it was dyed then, which may explain why it was longer - you cant really dye really short hair.
By the time he he reemerged in 2002 for the fall tour he was back to his natural color, and in 2004, the gray was quite obvious.
I think at one point in time, he may have. However, I believe once he embraced the aging process, he went natural. Now, he simply prefers to let the seasoning of his salt and pepper add to his overall flavor. Gotta love him for that.