Will it hurt my masters application if SOP focuses on my research interests, but the program has only a few courses on that subject? I want to pursue a master's in Computer Networks with an interest to learn Software Defined Networking. For some of the universities that I have applied, I have summarized like 'I would love to go deep into networking particularly software defined networking' Now will this be a negative if the colleges have only few courses on the subject?
Talking about your specific research interests in a SOP is great. If the specific interests are a good match for the program, they'll love it. If they are a poor match, you probably wouldn't have been happy or gotten the training you wanted in that program.

More importantly: Take a deep breath. (1) Your SOP for a masters program is not going to be scrutinized as closely as you seem to imagine. You are overthinking things. (2) It's too late to do anything.

Good luck!