I have done some research on how to access Blender's material nodes via Python and ended up writing a solution which address my original issue, I will post the code to serve as a possible answer.
However I am not marking this as the best answer because as Rich Sedman pointed out, Blender 2.8 already fixes the node setups when opening a .blend file. So maybe in some future release of Blender it too will address the nodes when linking and appending from external .blend files.
In the time being I must use this script in my custom import and automation scripts to fix the shaders after all models have been appended.
FixDisplacementNodes.py
#!/usr/bin/env python
# -*- coding: utf-8 -*-
__author__ = "Grant Olsen (2019)"
__credits__ = ["Rich Sedman", "batFNGER"]
__version__ = "1.0.0"
import bpy
"""Given a material this will search for any RBG to BW nodes that are connected to a Material Output's Displacement input.
If the RBG to BW node exists then this will create the proper Normalmap to Displacenment map node setup and replace the
RGB to BW node with them by linking the nNode to the dNode, then from the Image texture to the nNode, and the dNode
connects to the Material Output node. Finally it deletes the disconnected RGB to BW node.
"""
def FixDisplacementNodes(mat):
"""
Explanation: this function takes one arguments: `mat`.
`mat` is type bpy.types.Material and is the material for the object
to be checked for any RBG to BW nodes connected to the Material Output node.
Will replace with proper normal map node setup.
The return type is `None`.
"""
if mat is None:# an object can have an empty material slot where slot.material is None
return #nothing to process
for link in mat.node_tree.links: #loop over all node links for this material.
if type(link.to_node) is bpy.types.ShaderNodeOutputMaterial: #check if this node is connected to the type: "Output Material" node
if link.to_socket.identifier == 'Displacement': #check if this node is connected to the "Displacemnent" input
if type(link.from_node) is bpy.types.ShaderNodeRGBToBW: #finally, is the child node an "RGB to BW" type node?
bwNode = link.from_node #store the RGB to BW node for deletion later
dNode = mat.node_tree.nodes.new('ShaderNodeDisplacement') #newly created Displacement Node
nNode = mat.node_tree.nodes.new('ShaderNodeNormalMap') #newly created NormalMap Node
mat.node_tree.links.new(nNode.inputs['Color'], link.from_node.inputs['Color'].links[0].from_socket) #connect the Image Texture node to the Normal Map node
mat.node_tree.links.new(dNode.inputs['Normal'], nNode.outputs['Normal']) #connect the Normal Map node to the Displacement node
mat.node_tree.links.new(link.to_socket, dNode.outputs['Displacement']) #connect the Displacement node to the Material Output node
mat.node_tree.nodes.remove(bwNode) #delete the unlinked RGB to BW node
"""Loop through all objects in the scene, and for each object's material slot, passing it to FixDisplacementNodes.
"""
if __name__ == '__main__':
for mat in bpy.data.materials: #get list of materials, will save fixing same material for each object
FixDisplacementNodes(mat)
#for ob in bpy.data.objects: #get list of objects
# for slot in ob.material_slots:
# FixDisplacementNodes(slot.material)
Result:

[EDIT]
I am not sure which way is more preferred (if there is even much difference) but here is a variation which exactly replicates the way 2.8 converts the shaders when opening a .blend file (notice how it keeps the RGB to BW node):
FixDisplacementNodes.py (v2)
#!/usr/bin/env python
# -*- coding: utf-8 -*-
__author__ = "Grant Olsen (2019)"
__credits__ = ["Rich Sedman", "batFinger"]
__version__ = "2.0.0"
import bpy
"""Given a material this will search for any RBG to BW nodes that are connected to a Material Output's Displacement input.
If the RBG to BW node exists then this will create the proper Displacenment map node setup and link it to the
RGB to BW node.
"""
def FixDisplacementNodes(mat):
"""
Explanation: this function takes one arguments: `mat`.
`mat` is type bpy.types.Material and is the material for the object
to be checked for any RBG to BW nodes connected to the Material Output node.
Will replace with proper normal map node setup.
The return type is `None`.
"""
if mat is None:# an object can have an empty material slot where slot.material is None
return #nothing to process
for link in mat.node_tree.links: #loop over all node links for this material.
if type(link.to_node) is bpy.types.ShaderNodeOutputMaterial: #check if this node is connected to the type: "Output Material" node
if link.to_socket.identifier == 'Displacement': #check if this node is connected to the "Displacemnent" input
if type(link.from_node) is bpy.types.ShaderNodeRGBToBW: #finally, is the child node an "RGB to BW" type node?
bwNode = link.from_node #the RGB to BW node
dNode = mat.node_tree.nodes.new('ShaderNodeDisplacement') #newly created Displacement Node
mat.node_tree.links.new(dNode.inputs['Height'], bwNode.outputs['Val']) #connect the RGB to BW node to the Displacement node
mat.node_tree.links.new(link.to_socket, dNode.outputs['Displacement']) #connect the Displacement node to the Material Output node
"""Loop through all objects in the scene, and for each object's material slot, passing it to Check_Material.
"""
if __name__ == '__main__':
for mat in bpy.data.materials: #get list of materials, will save fixing same material for each object
FixDisplacementNodes(mat)
#for ob in bpy.data.objects: #get list of objects
# for slot in ob.material_slots:
# FixDisplacementNodes(slot.material)
Result:
