You don't need to remove the switch to get rid of the warning, you just have to disconnect it. On some models A4 the detector is part of the latch mechanism, on others (depending on model year) it's on a separate push-in catch near the latch. You can see a cable going to it with a modular connector. Simply pull the connector apart and secure the ends so they can't get sucked into anything. I don't think you need to jump across the wires to get the light to stop, so try it without wiring them together first.
If it's a separate switch from the latch it may be that the switch has just come out, or maybe the plastic bracket that retains it has broken. You may be able to just pop it back in.
I don't think that the wipers are in any way connected to the hood sensor, on my A4 I ran the wipers with the hood open several times on all settings. I think you have a separate issue there, probablypossibly the selector mechanism, although that wouldn't explain the in motion thing. Maybe it's a relay, I'd check the simple things first.