All that may be true, and I'm not disputing any of it. But all energy sources and storage methods have their drawbacks. They're not necessarily a reason to something out. I'm sure Hydrogen will play a role in certain areas (e.g aviation and steel production). The tech is still young so there's bound to be significant developments coming.
There are numerous studies on the NOx levels produced by combusting hydrogen in air and they all show levels much higher than those associated with methane (and methane NOx emissions are already recognised to be be health threatening in urban environments) because hydrogen burns at a higher temperature which promotes the formation of nitrogen oxides.