For examples sake.. What if someone changes their ms specc to for example enhancement and rolls for that type of gear aka "Mail agi gear", but the player does not even play this specc, the player has dual specc with elemental in one and resto specc in the other. If the raid leader then gives the item to the second highest roller, lets say an actual enhancement shaman or hunter. Is this then considered ninja looting?
IMO it's a valid MS change. Just because he doesn't have it active atm doesn't mean he's not gonna or doesn't plan to have it further down the line when he gathers enough gear.
Also, keep in mind some people have gear for 3 specs (1 DPS 1 Tank 1 PvP for example), and then they just switch talents as they need it.
Without having specific limitation of "MS changers has to have talents (as well and gear)" set up by PUG leader, this is perfectly fine. As RL/ML, I'd check if he came with hunter friend, if he did, they might aim for gearing that hunter with two rollers. If this feels unfair, then I'd remove them.
Well, okey another question. If the RL then gives this item to second highest roller? Is this considered ninja looting? And can the player receiving the item get banned for this? Or is this entirely on the RL?
It would be considered ninja looting in that case, yes. It's entirely on the raid leader (master looter).