while I don't have an aftermarket rack, I do have crossbars with two pelican cases up there all the time. the shape of the crossbars ultimately will determine whether you have noise. square or round crossbars with nothing on them (especially ones with cutouts for gear) will make noise. it's called the aeolian noise effect. a wind faring will drastically reduce this but won't eliminate it. you could also use a couple eye-bolts in the empty bars as well to disrupt the airflow. obviously other factors such as tires and radio volume and your own sensitivity to noise will play a part as well
if you load gear on a flat crossbar and there's a space between the gear and the bar you might have noise as well. generally though if you have gear on your crossbars the noise will be less because you disrupt the airflow over the bars. this is to some degree because putting something like a RTT up there is just so big it catches air. if you have low profile boxes, or boards etc. you probably will reduce noise
I would highly advise against running empty square bars with no faring. I run two thule 60" bars and they make zero noise. with two pelican cases up there I still get zero noise. maybe because the cases have ribs on the top which helps disrupt the airflow over the top. my pelicans are filled with stuff I'd rather not carry around in the trunk (fire extinguisher, compressor, hose lines, cables, shovel, med pack, etc. etc.). Like others have said I got rid of the two bottom layers of foam, used some grippy rubber workbench liner and kept the top foam. keeps things from moving around