[Arakon]

from the looks of it, removing the component just totally disables the USB port, so it's safe to do.. unless you ever plan on using that port again. if you ever plan on using an USB mouse + USB keyboard (i.e. for webbrowsers or unreal tournament) on your PS2, don't remove that part.
I highly recommend getting a decent modchip.
and yes, you have to patch any and all EA-style protected games.