I think maybe we should get someone from the SNS team on hear explaining why the SNS wasms (not deployed SNSes) needs to be at the system level and not at the application level.
To answer this particular question: It would have been an option to store the wasms directly on the SNS subnet. In fact, this was our original design proposal. The main reason, why we changed this design (see this post) is that having it on the NNS allows us to have one place with all the relevant information even if there are multiple SNS subnets in the future.