Do these "draft" calculations include the rudder, prop, and skags?
Yes, but they should also tell you the speed, weight, trim and deck angle or rise needed to achieve that. The rudder and or prop are almost always the deepest points. Regardless of what may be posted on a website, the swim-deck on most boats just sits above or at the water-line. So measuring from that point to the bottom of all dangling items will give you a good idea of what it really is. Of course, the boat will squat when under initial acceleration and will rise on plane. If the water is low, don't go, go somewhere else or go dead slow to prevent major structural collateral damage and check depth frequently with a calibrated pole.
For the OP, if it is just deep enough to run safely, it still may not deep enough to board or surf safely. You don't want to take a header into the creek bed! As well, you need somewhat deeper water to develop a good surf wave.