Probably because it's both easier to make and more visually impressive and interactive. Contour maps made the naive way are too noisy, you need to process the height data in some way first. With 3D all you need is to put a vertex in each height data pixel and use the value as a z position.
https://hkartor.se/anteckningar/generating_graceful_contour_...
http://routegadget.net/karttapullautin/