When disturbing substrate there are a couple of things that can happen. One is indeed toxins like hydrogen sulphide being released at once. When into the water column, it pretty much evaporates/ makes a reaction and is neutralized but on it's way out of the water it may affect fish if you released too much at once and fish were in the way. However, it's more harmful when bottom feeders dig into the substrate rather than anything else.
The other issue is an ammonia spike which normally follows when one disturbs the substrate way too much. In both cases when you do that, you need to follow with a large water change or two. Then it should be pretty much safe for the fish. This is more likely the reason your fish died? Have you measured the ammonia/nitrites?
And why having a deep sand bed?
Siphoning a deep sand bed will not prevent either of these issues happening in the future. Sand compacts back within minutes. When the substrate is deep, it doesn't get enough oxygen into the bottom layers and anaerobic decomposition occurs. Anaerobic decomposition causes the production of harmful gasses such as hydrogen sulphide and others. It stays in there if you don't touch it, but once you disturb it, all this can go out at once.
If you have a thin layer of substrate, then because it gets oxygen, aerobic decomposition occurs instead, which produces CO2 instead and not hydrogen sulphide or at least not in high amounts. The CO2 as you know pretty much goes straight out via the surface agitation and doesn't harm the fish.
Both processes also produce ammonia. Disturb any substrate, it goes out into the water column. Siphoning can reduce the amount of organics those bacteria use to produce ammonia and gasses but to be honest it's impossible not to have organics in the substrate. Siphoning only helps to keep the substrate aerobic to an extent as it doesn't get clogged to the point of oxygen not reaching there.
And this sort of setup where one has "oxygenated" substrate is healthier for at least bottom feeders as it also doesn't promote harmful bacteria that may directly affect fish.
Best way to get nitrates out of the water is water changes and not a deep sand bed in which what happens one can't control.