Well the non-manifold issue has been around since before it was included in maya on heatmapping. I tend to not use heatmapping "heatweight" in cases where geometry is not sealed. It mainly has to do with how it determines falloff with heatmapping. The process is as simple as maya goes and jams thousands of balls into your mesh and based on amount of marbles from said joint location it determines the falloff rate and how it will affect the joint in terms of weighting. As you can imagine this becomes a huge problem when a hole is in the mesh because it is generating that falloff infinitely. To read up more on heatmapping look up the SIGGRAPH documentation on "Pinocchio" from about 2008. Hope that helps. Otherwise you will just have to seal the hole or get your hands dirty with traditional weight painting methods....