It took some tweaking, but I finally got my shop vac working without killing the bees. I screened over the drain hole at the bottom, rather than keeping it sealed, and I taped some big-cell bubble wrap to the surface that the bees hit when they come in from the tube. I also reduce the exhaust hole by about 3/4 with duct tape. I'm not using a smooth tube; the stuff I found that was smooth was super heavy and not at all manageable.
Buy extra tubing, too, so the vac is far from the hive. Mine came with a 7' tube, and I bought two more. I usually only use two, but if I need the extra reach, I add the third.