Will it affect anything if i remove the heat shields for the exhaust system. I want to get rid of this rattle but ruining something else isnt what i have in mind.

 

you should be fine, i did the same thing on EJ1 b/c of a rattle and never had a problem, IMO they dont realy even serve a purpose, they call them a heat shield but they get nearly as hot as the exhaust manifold itself, so to me they are pointless