I'm not sure people are understanding the sheer scale of a multi year intercontinental war between superpowers. Using WW2 as a rough equivalent, even smaller campaigns are going to have five figure casualty lists for each side. The bigger ones will be more like six or seven. Multiply that by at least nine years of war, and DG's official hat as a medical facility, and it's not quite as hard as you might think for a few thousand people to disappear, especially if you have a good propaganda machine. Call them back for treatment, then say 'sorry, we did everything we could, but they were too far gone/the wound got infected/we had an outbreak of X disease', and you only have to do that if someone actually asks for an explanation.
Deepground also is entirely composed of SOLDIERs, even though only a small amount of the population is capable of becoming this. Literally no one living in Nibelheim was capable of enduring a SOLDIERs treatment, Cloud was the only one that could come even remotely close. Every one of those thousands in Deepground is individually a stronger person then Cloud, let alone anyone else in Nibelheim. It's not like they were able to create this army by disappearing entire towns at a time, they were each carefully handpicked.
Source for all this? The SOLDIER in Deepground were the ones with the swords that aren't in heavy armour. SOLDIER have to be carefully handpicked if you are worried about side effects to their health or sanity, if you're not, you can bruteforce it. And the rankers on the ground are nowhere close to Cloud, we see unenhanced like Reeve and Shalua are able to kill them easily enough. And they all suffer the side effect of needing Mako to live.
Also Deepground is better equipped then the entire rest of Shinra combined. They got more robots, tons and tons of combathelicopters, better combat gear, better computers, the works.
Not close to true. DG has one model of helicopter (the Dragonfly) and one model of armour (the Black Widow), which they tweak a bit, but are stuck with. They have small numbers of red saucers (which are super easy to destroy), a handful of sweepers, and not much else. The hover bike/jet pack units are present in such small numbers they only show up for one boss encounter each.
They have no special ammunition, no grenades, no materia (except the commanders). They have no Guard Scorpions, no Carry Armour, no Hundred Gunner or Motor Ball. No tanks, no autonomous gun turrets. The officers in the ordinary Shinra army (red soldiers) wear something like full plate armour and carry laser guns. In addition, Hojo has stuff like H2so4 and Behemoths available to him. There's also stuff like 1st Rays, those weird rose looking things that cast magic, Moth Slashers, and a lot more. Mighty Grunts in heavy armour, Aero Combatants...
The only reason they have better computers is because they need it to contain DG.
Shinra was a weapons manufacturer, they are going to have tons of weapons lying around, especially after the war when the army gets scaled down after the war. But they don't let DG near their best gear.
And yet when the entire planet was being threatened Heidegger and Scarlet were not at all interested in using any of this to save themselves. It's not like they didn't believe in the threat either. They saw it all, Sephiroth, the WEAPONs, Meteor with their own eyes. They had a good week before Tifa even woke up, another week or so till the day of Meteorfall.
There's no situation where DG would be useful in FF7 until Sister Ray knocks the barrier, and Heidegger, Scarlet, and Hojo are dead very shortly thereafter.
built underneath a city, without anyone involved in Midgar's construction knowing about it. It has a reactor that no one knows about. mountains of food is brought there that no one knows about.
Was it? Is the reactor itself a secret? Nobody seems surprised to hear about the reactor itself. Built, then forgotten about seems more likely, because the prez thought it would be cool to have a secret basement. It started as an ordinary medical facility, which people likely knew about, and then were told was shut down after the war. Tell them the Shinra building needs its own dedicated reactor, which for obvious reasons needs to be heavily protected, and you justify a lot of the traffic headed down there.
Here's the script:
Reeve: The whole organization was kept a secret. That is why there is so
little information on them. However, it's nothing like I expected.
Vincent: Not even a person in your position was informed?
Reeve: No. Other than the president himself, the only people who knew of
Deepground's existence were most likely Heidegger, Scarlet, and
the head of biochemical research, Hojo.
Reeve: After the president's death, the transfer of power to his son was
carried out so quickly, I doubt Rufus was ever briefed on the project.
Reeve: As for me, I was told the information was on a need to know basis. And
as an official in charge of urban development, I guess I wasn't on their
list.
This is Reeve guessing, because he wasn't involved. The implication I'm getting is that he knew
something was going on all the time, but was never told the details. Given Vincent's preceding question, he could be talking about only the executives that knew, and he's only guessing anyway.