Will the emitted radiation and / or particles change if say two neutrons are collided inside an accelerator at different speeds ? eg) 0.95 c versus 0.99c

Yes. The amount of energy involved is massively different between the two situations.

Yes, because of the much greater kinetic energy at the higher speed. This is why larger and larger accelerators have been built. Higher energy allows smaller sizes to be probed.

http://www.slac.stanford.edu/pubs/beamline/27/1/27-1-panofsky.pdf

 

(But note that you can't accelerate neutrons as they are uncharged.)