This isn't answering your question necessarily, but I like to imagine the discrete features as a secondary model domain. The primary (elemental) and secondary (discrete) domains will have the same values of head and fluid flux at the nodes, but use different laws and properties to define flow between the nodes.
A vertical fracture, as you have described, will 'connect' the 4 nodes on the vertical face of an element (assuming in 3D), with properties specified by you, but depending upon what law you are using to describe the flow. For Darcy, it is conductivity, thickness (aperture), etc.