It would be more helpful if people indicate the brand of intake manifold that they are referring to.
The Fenton and Offenhauser intakes have a few significant differences, one of which is mentioned above.
Another difference could be important relative to the type of heating plate one obtains. A flat inside/upside-surface on the "heat plate" is preferred on an Offenhauser but makes little difference on a Fenton intake.
The Fenton intake does not have journals that allow gas/water to flow from one-side-to-the-other-side of the intake, so it does not matter if the plate is flat on the inside. Because of this, I see no benefit from running water; exhaust gas heat would be just as affective (and, easier to plumb and no worries about future problems with long lines). Exhaust-gas or water, heat is moving through conduction not flowing throughout the manifold.
The Offenhauser has a divider ridge that should mate against the heat plate - this allow true flow. This intake benefits from using water flow (as long as you seal the plugs, which need to be sealed for exhaust-gas, too). Exhaust-gas (from Fenton headers, for example) would not truly flow in this set-up; however, coolant water coming in one side and going out the other side provides heating via a flowing liquid (not just conduction).
