There is definitely a sound difference in aftermarket intakes. The stock intakes have those odd shapes because they are tuned to be quiet. Those shapes are resonaters and cancel out the sounds made by the rushing air (I dont believe they are to trap water). The typical CAI is a curved pipe, and you WILL hear the air moving through it.
Hydrolocking is a concern in STANDING waater. It would take lot of rain to cause isues. I've had CAIs on all my vehicles for 15+ years without a problem. If you read through posts online you will find hundreds of people with CAIs and maybe 1 or 2 with issues. its just a CAI, not a 500 shot of NOS.
To Maduro, Put on the CAI and enjoy the improved thottle response and cleaner engine bay. You wont have any issues. Dont sweat the filter cleaning, just do it when it needs it (probably a lot less frequent that 3500 miles). Just use enough oil to color the fabric, dont soak it in oil.