ADB pull fails to pull folder that exists
I want to post this answer for future reference in case anyone experiences this problem. I was unable to pull the folder system/etc/wifi/ using adb with root privileges until I booted into recovery. 

I was using TWRP 3.0.0-0 and I was then able to access adb in TWRP and then pull the folder in question. I am unsure of why the folder was not pullable in the first place but pulling it from recovery works.

Commands successfully used in recovery

adb pull system/etc/wifi