Are you saying that the local soil/water conservation district (aka the ag people) are reviewing NPDES permits in your area? That's a new one for me.
On the other hand, it's not unusual at all to have non-licensed engineers reviewing plans and calculations. Most state and local governments just don't pay enough (and can't) to get a PE for that kind of work. You would hope, however, that the reviewers are supervised by a PE. But in local government offices, politics often trumps common sense, and "some one else" is often overseeing the work of the reviewers and inspectors, while the PE either has no authority to supervise, or isn't even there at all.
Yes. The local conservation district has a deligation agreement with the DEP.
For land development purposes, only individual permits are kicked up to the regional DEP office.
In PA and Jersey, in my experience, all reviews on the local level are signed off by a PE (whether in house or subbed out as an agent for the Township), with the exception of the DEP and PennDOT.
I am OK with the transportation signoffs b/c the majority of the regulations have been around forever, so very little interpretation is required. But even PennDOT will sub out their stormwater reviews to a PE.