PhysX does have a footprint in general RAM, it's not entirely GPU bound. But yes I agree with your general points here. As mentioned I'm not sure what if any actual die space has been saved by removing 32bit support, it would be odd to remove it for literally no reason.
More importantly I fully agree Nvidia should have done something. Software emulation or providing a patch for old games PhysX would be the right thing to do. Heck, at least a more detailed statement of why they've done it is better than the silence we've had.
To be clear I'm not defending Nvidia's move, just trying to find some logic as to why they removed the support for it.
Reason is simple, no need for updating the software anymore. Also they did same with SLI.. removed it without warning on 30 series.