My 3 year old son has been taking loratadine for hayfever for the last 2 weeks and in that time has developed a stutter which got progressively worse?

Likely unrelated. 3yo kids often go through a transient period of stuttering that may last a few months. I can't attribute this to the med because it doesn't enter the brain like some antihistamines do. You can certainly stop for a few weeks and see if it fades and restarts when he is on it. That would be cause/effect evidence. If it just fades when he comes off you won't know if it would have anyway.