Does Batman have unlimited ammo

Shoot a Remote Electrical Charge directly at her head. It should pop off and count it as completed.

You can't use explosive gel above your head unless you're able to climb up really close. In both of these cases, you need to get on top of the structural weakness. Careful exploration of the room in your first shot will reveal a way up; your second example will be in your way as you're heading for Hugo Strange. Don't worry about it until then.