I'm sure that using a perf screen is not a good idea in many HT configurations. I have made a comparison at a local HT store (the projector was a Sharp 9000) and I have two comments. First, I noticed no moire whatsoever (I'm not sure whether the Cygnus lens was present, but they do sell that product). Secondly, there was a distinct and objectionable high frequency rolloff when the screen was lowered.
The dealer admitted to this but claimed that most people never notice the effect. He also said that Stewart includes special equalization networks with the perfed screens to overcome this loss, but he could not install such with the particular surround receiver in that demo room.
The root cause of the problem is the perfs for HT screens are very much smaller than those in commercial theaters, and the high frequency attenuation is therefore greater.
If you are using seperate processor and audio power amps, I guess this is less of a problem, because you could use the equalization networks. Alternatively, you could conceal the speakers behind acousticly transparent panels above or beneath the screen, and make use of the fact that human directional hearing is virtually all in the horizontal plane.
What I did was conceal the three front speakers and subwoofer in cabinetry underneath the screen, and used cabinet doors where the panels were replaced with speaker cloth grilles. Then I removed the grilles from the speakers themselves and the result was balanced sound with the dialogue effectively anchored to the screen. The only problem I had to overcome was a few cabinet rattles from the subwoofer, easily fixed with some extra screws and some stick-on felt pads.
Gary