Hive two has a lot of brown "poo" on the front of the hive. Can this be nosema?
Maybe
Is there a difference with bees just having the hershey squirts and having nosema or is it one in the same?
Yes, the dark brown "poo" is a sign of dysentery. With dysentery, the bees may or may not have nosema. To diagnose nosema you need to view the bee internals under a microscope.