Yes, it has, and prj files are not included as a node, or installed, as I understand it.
Yes, 'prj' files are gone at 10.1. From the Python perspective it shouldn't matter much, we will still 'recognize' the files even though they don't technically exist. So if you used a direct path to one of the installed prj files at 10.0 as input to the SpatialReference class--it will still work at 10.1 as it did at 10.0.
A few better options at 10.1 though, the sr name or factory code will work as well. -Dave