I don't think that the von Neumann boundary conditions are used as default: by default, no term is added to your variational form.
If you're solving a Poisson and don't specify any boundary terms, then indeed it is equivalent to specify ∇u⋅n= 0 on the boundary.
But if you're solving an advection equation, then not specifying any boundary terms will be equivalent to specify u = 0 on the boundary.
Thus, my understanding is that FEniCS will by default not use any boundary condition.