In my limited experience, a stock trailer will be much louder than an enclosed trailer. Think about how much louder a convertible is verses an enclosed vehicle. Over time, the convertible will also develop more rattles and wind noise because it isn't as stable structurally. I would assume the same might be true for a stock trailer verses an enclosed one. Lastly, stock trailers are generally lighter trailers and they will bounce a little more on the roads, causing more rattling and noise.

As a compromise, you might consider looking at a stock / combo trailer rather than a straight stock trailer. It should be a little more quiet and have some insulation to buffer noises.

I used to haul my arabians in a stock trailer. If anything they became more acustomed to the noise. I don't know if the really bounced around more than in the current GN trailer or not.

Perhaps they aren't getting nervous about the ride but the destination?