What you say describes what the JP Aerospace folks are doing, and it's a pretty neat system. I only wish I could find more about it online, but alas, the JPA website and the affiliated YT channels (plus some random references here and there) are all that I could find. In any case, as we said, these Ascender/ ATO vessels seem to be derivatives of the military models (due to how it's probably illegal for companies to test aircraft with nuclear reactors on board!) and as such do not have similar capabilities.
It's true, dirigibles that gain power from onboard batteries or solar cells, and propel themselves with either dirigible motor engines (as with some of the heftier Ascender models) or a series of modified chemical rockets (as with the monster ATOs) would take days to achieve top speed, and might be fairly noticeable. However, a vessel like the reported "TR-3B"s and other black triangle/ boomerang craft seem to be powered by compact nuclear reactors, which provide the required high amounts of energy to ion engines (whose function is described above), which seem to be able to accelerate and decelerate faster than more conventional means. Me and my colleagues are keen to try and figure out how fast they can go, how quickly they can achieve speed or stop, and how much power these operations demand.
We are aware that the bane of most conspiracies and cover-ups is the amount of people involved. Tbh I have no good answer to this, besides offering the possibility that perhaps less people are involved with this than we think (beyond some engineers, technicians and airbase personnel). I can't see deflating a dirigible being too difficult.
Chances are you could compartmentalize handling the indirect (as in storing) handling of vessel components so that nobody really knew what exactly they were dealing with, and intimidate any others into silence. Since the military does operate on a strict need-to-know basis with projects of this nature, and coercing a technician into silence by threatening his family would be effective, I could imagine these things being covered up quite adequately. Any whistleblowers who slip through security can just be called loonies and conspiracy theorists. That's just for handling these vessels. As for designing them, that's even easier to covver. Teams of scientists could work on separate components, and you just have one small engineer team combine the results. The origins of the technology used in these craft (like compact reactors and ion technology) is desperate throughout aviation history, and would have been easy to source because of this. As for manufacturing, we know from THIS interview with the founder of JP Aerospace that companies have been making stealth dirigibles for decades. Just because no-one "blew the lid" on these projects doesn't mean that they don't exist!
I would argue that these craft, and modern spy planes like the X37 or SR-72, are completely different in nature and operation, and thus the prerequisites for observing and imaging them cannot be compared. As you say, the X-series spy planes aren't really much of a secret. Their origins and plans of construction were fairly well-known, and their test parameters are fairly easy to predict. If you had modern equipment (as the fellow who captured the test being done had), it should possible (although exceedingly difficult!) to find and capture footage. These factors do not apply to the "black triangle" craft.
First of, the public has little to no knowledge of their existence, and so cannot predict where to look for them.
Second of, because the bulk of their testing (presumably) took place decades ago, AND was mainly in the high atmosphere OR close to the ground in remote areas, it would likely be impossible for anyone avid enough to try and spot secret government technology to observe these vessels with the equipment of the time that was available to citizens, much less capture good footage of them. That is not to say that we of course never see these. As my original post states, these things are apparently subject to malfunction, and may descend during such an event. Thus, people can see them, although the craft seemly manage to get away before good footage can be captured. Rather like ball lightening, the event is too sudden and alien for people to adequately react to.
Third, the black triangles and boomerangs do not fly like planes, and as such cannot be anticipated to have footage captured of them in the manner one may capture footage of a low-flying spy plane or nigh-space bound space plane.
I strongly argue against sightings of these craft being misidentified airplanes or helicopters. I DO acknowledge that many sightings of these craft may have been faked, due to their prevalence in the UFO community, and that certain unqualified observers might mistake them with normal aircraft or natural phenomenon. But the cases of mass sightings, along with reports made by highly-qualified observers (like pilots or military men) are hard to counter with saying that these people are lying or delusional.
Take the Phoenix Lights for example. These were stationary lights in the sky, apparently emanating from a completely silent, but huge craft. Take a look at the original footage for yourself (apologies for the terrible quality, it was 1997 after all):
And compare to what happened when the airforce tried to recreate the scene with combat flares:
In case you think the above video is biased, check out these flares (you'll notice how quickly they fade in comparison to the Phoenix Lights, and how different they look):