@ecto I tried your suggestion and added -sndspeed 44100 to the emulator.cfg file but it is still crackling however it did seem better.

On another note I think I figured out how to change the install script to build and install the hexen 2 sdl2 version.

download the install script using tpo1990's provided command:

wget https://raw.githubusercontent.com/tpo1990/Hexen2-RPI/master/hexen2.sh -P /home/pi/RetroPie-Setup/scriptmodules/ports/

Go into RetroPie-Setup/scriptmodules/ports folder and the script is named hexen2.sh

Edit the script find and and change https://github.com/svn2github/uhexen2.git to https://github.com/jpernst/uhexen2-sdl2.git
save it
go into the retropie settings in emulationstation,
go to manage experimental packages
select hexen 2,
install
then reboot the system or just restart emulation station after its done, and its good to go.

Tell me if I'm wrong but it seemed to work for me.