Yes, the implementation did change; I do not see any release notes saying so, though.
I see in R2016b that non-separable filters have two branches: filterSingle2DWithConv() for single(), and filterPartOrWhole() for everything else. filterPartOrWhole() calls mex routines to do the work. You are using double(), so you would get the "everything else" mex routines.
I see in R2017a that non-separable filters have three branches: filterDouble2DWithConv() for double() for 2D arrays; filterDouble2DWithConv() (same routine) for double() with 3D arrays; and filterPartOrWhole() otherwise. (Notice filterSingle2DWithConv is gone and handled by filterPartOrWhole() now.) You are using double(), so you get the new filterDouble2DWithConv() routine. It calls upon conv2() to do the work.
I think you would be justified in filing a bug report on this.