Sacrificing Deus Ex to the gods...

[Tuftears]

I've been playing DXHR stealthy/nonlethal! (Pacifist achievement: kill no one other than the regrettable boss fights) I would say, you don't want to try to line up your shots on the enemies unless they are facing away from you. If they are facing you, they'll see and shoot you quickly. Cover seems fine, great even-- when used for stealth. As you say, your accuracy will suffer a lot if you can't line up your shot with the ironsights/scope.

There's an automatic inventory manager so you don't have to worry about your inventory much, except for not having enough space.