It needs to be a thin one. Wireless charging usually requires the device to be within a couple millimeters.
If your case stores your credit cards on the back of the phone like I do, yes.
I bet you the Apple cases don't.
It depends on the characteristics of the case and how far it stands the phone off from the base.
For what it's worth, my last phone with Qi was a Blackberry Priv with an Otterbox Defender case, and it charged just fine. I'd be very surprised if Apple didn't make allowances for something that common.
On my Samsung S7 the (relatively thick) case doesn't block the wireless charging.
I have a regular UAG case and it allows wireless charging just fine