You can create a mask for the smart filter or you can "stamp" (ctrl-alt-shift-e) the SO, convert in NIK and put a mask on that layer. The problem with masking smart filters is that within an SO, the smart filter mask applied to all the filters, at least AFAIK. You could open a SO from LR, stamp it, mask it, then create a new SO from those two layers, and you could still get back to your original LR adjustments by opening the nested SO. First two options above are easier.