If following were true:
a. ‘Water-Elev’ = 0m (i.e. at origin)
b. ‘Wave-Height’ = 5m,
Does this mean that the wave crest will be ABOVE 0m (origin) as it appears in the diagram above?
As indicated in the image above, Yes, if the original surface elevation was set to Vertical axis = 0m and the wave height = 5m, then the crest of the wave will be at Vertical axis = 2.5m, which is above the Water elevation.
How does AutoPIPE account for buoyancy of pipe elements between the wave crest and the water elevation (i..e yellow shaded area in diagram below)?
Per AutoPIPE help for Water elevation and Buoyancy:
Water - Elev.
Enter the mean elevation of the water body surface. The elevation specified is relative to the origin of the global coordinate system. All points with a vertical coordinate value less than the elevation specified in this field will be considered submerged.
Under hydrostatic loading, submerged piping is subject to an upward buoyant force (Fb)
Therefore, piping in the yellow area will not be affected by Buoyancy Loads settings because only Water elevation would be considered and not the Wave Crest elevation.
"Wave" - Load Case