Well, no. Laws are only created by Congress. Regulatory agencies can create non-trivial policies, and you might want to argue that the distinction between a regulatory policy and law is minimal or non-existent. But regulatory agencies are never what proponents of the deep state are discussing in my experience. Likewise with judges - and if we wanted to somehow include judges in the deep state, we have the problem that Trump has at this point appointed more federal judges in a single term than any other president and more SCOTUS judges than any other president. If judges are part of the deep state, Trump can not in any way be said to be fighting against it.