Per the article, the main issue with Project Mogul is that the detection equipment wasn't reliable enough to confirm the channel (even just getting a weather balloon to stay at a constant altitude is difficult); the project fell into the low-priority list for military research and (due to being classified until recently) wasn't visible to the general public.

Even now, researchers have only detected "signs" of an evasive channel; it appears to be far more inconsistent than the analog in the ocean (which makes intuitive sense, since pressures and temperatures in the atmosphere are far more variable than in the ocean).