#1
my thumb muscle [bottom left of my left (fretting) hand] had been acting up after elongated playing for a few days, so i decided to trying playing with my hand on the back of the neck for a bit. i wanted to play more with my thumb on the low E string and i wondered if this would be helpful for this?

can it be bad for me playing in both this and another fashion? or any other draw backs or what have you
#2
no it's fine. for metal i put my thumb on the back of the neck, but for blues and other stuff with feeling in it i put my thumb on the low E (there is some switching back and forth), plus it helps with bends.

GUITARS CURRENTLY USED
Ibanez RG7621
Ibanez RG121
ESP LTD H-400
#3
not an issue as long as you are not pressing down very hard with your thumb.

placing the thumb on the low E can help with muting and adding certain bass notes to some chords so it is actually very useful