Hi mate. It’s probably the most common mod here in Australia with a HDJ100 - to put a 3 inch exhaust on the car. It does help it breathe a bit better and gives a small improvment. Some keep the muffler, but some people just have a entire straight through exhaust - which is usually super loud.
I removed my centre muffler, which had an amazing about of soot (no cats here in NZ for a ‘99 cruiser) and left the resonator at the back. Noticed the low down performance straight away and the sound is fine. Gives it a nice deep rumble.
Been considering a full turbo back 3inch system. Pretty much straight pipe but have no idea how loud that would be. Being a turbo shouldn't be deafening. Was considering a decat as a tester but thinking now you have bitten the bullet it's not worth it and may go down the full system route...the only question is to resonate or not to resonate