Its actually quite easy to remove. Go through the wheel well. Jack up the car and take off the pass wheel. Its a couple screws and push pins and then you can peel back the liner and you will see it held in with one bolt. Take out the bolt and pull it out.
The Resonator is designed to redirect your airflow many times to capture water. To do this it has pockets. Your stock box is sealed
so it has to capture water before it gets to it.
You shouldnt have water that far up your quarter to begin with but that is the purpose of the resonator.
With a cab intake there is a difference up top which negates the need for the resonator...
It not only negates it but the resonator then restricts the air from the quarter since nothing is connected to it to pull (vacume) air up through it.
The Crab intake shield is not sealed at the bottom. It allows any water making it into the box to run right out. The filter is suspended inside the box. Water has an outlet.
Take a quarter full glass of water and a straw.
Suspend the straw half the distance from the top of the glass and the water.
Now suck like crazy. How much water did you get?
Next cut a slice where the bottom and side of the glass meet and you have
a CAB. Where did the water go? You still sucking? lol
I would wager you got no water.
Well the filter is the end of your intakes straw. I cant see the cab being half full of water unless your in a lake but you get the idea.
Your stock setup extended their straw down into your quarter panel via the resonator. Once the stock box is removed the resonator is now just blocking air from entering the cab via the quarter since it is no longer connected to the intake system (vacume again....insert straw example).
The water issues are then resolved above the quarter as the CAB allows water to escape....where the stock box had no where for water to go.
With a stock setup I would leave the resonator on.
With a Crab I would remove it.
But this in no way means that you have to remove it.
You can leave it on if it provides peace of mind.