Let me begin by saying I'm NOT an expert. I'm still learning about how these turbo cars work. But this is my take on your questions.
Yes, when you replace the muffler you remove the CAT. That metal line isn't reattached to the muffler. You can just leave that open to the air. I believe that is emissions stuff.
Yes, you can hear your wastegate opening. It's not constant, but once in a while I can hear it. If you can hear yours constantly then yours may be stuck open. Also, if you aren't getting a consistent boost then you may have to address your wastegate. It should be consistent.
Read the link below and hopefully somewhere in there answers your last question. There is some good info in this thread, but more specific to what you're asking starts on page two.
Is this a K27 Turbocharger?