I just had my trykon set up by a hooter shooter at the pro shop with a string loop. Its a tad long with the loop. My question is if I remove the loop and put nocks on the string will the arrow still shoot the same?

It should, the only thing your anchor pointmight change a little.. Shoot it and adjust the sight if you have to. No a big deal.

Thats what I thought but I get mixed answers on it.

Yep I shot off the string for a long time and then switched to a loop and I was shooting high. but you shouldnt get any left and right differences unless your pulling the string harder to your face without the loop. If it feels better without the loop I say go for it. I shot great without one for a long time. Just adjust your site cause your probably gonna hit lower than you expected.