I don't think the noise is a problem once they are used to it, it all depends how the dog acts toward them. If he acts too interested, sees them as prey or toy, they pick that up.
It would help if the dogs are either introduced to the bunnies and teach them that they are just part of normality - depending on the dog if this is possible, or when the dogs can't go too close to the rabbits enclosure. They should not run there, excited about those interesting fluffy things.
As I said, it really depends on the dogs instincts, training goes only so far, if he isn't able to ignore the rabbits on his own once used to their presence I would at least put a fence some meters away from them. And they need places big enough to hide completly out if sight, hidey houses with at least 2 entrances (they avoid dead ends when stressed).
I had 3 dogs here over the time, from friends for some weeks, I had the advantage that when the dogs came here the rabbits were part of this new environment, not something that pops up in their territory. Also, my rabbits are free roam, and don't take long to approach a dog that acts unthreatingly.