Xenos can probably tell who a leader is based off of pheromones or something, power dynamics n shit, if you see one guy point towards something and shout and everyone around them stops what they're doing to do that, the shouty guy is /probably/ the leader, and xenos understand what leaders are
as for spec weapons, they know how they work generally, and since they're a hive mind it might not be unreasonable to think that the tube that one host pointed towards you all might be dangerous, though they probably wouldnt know exactly how it works or what the payload will be