The out-of-universe answer is obviously they weren't invented yet. I think we will probably see them more in new materials going forward.
In-universe, there just wasn't a lot of them compared to plain Stormtroopers. They are highly specialized troops that operate almost exclusively as guards for officers within the Tarkin Initiative. That means after Tarkin dies and the Tarkin Initiative is disbanded they were probably reassigned to other units.
Other limits to their numbers is the fact that the physical requirements are much higher than standard troopers. A small fraction of recruits are qualified to even go through Death Trooper training. Presumably not everyone that starts the training graduates.
They also have a great degree of cross-training, which is something the Empire doesn't like. That's one reason the TIE Striker wasn't seen in widespread use, the navy wanted ships that were specialized for one job.
Finally is cost. Death Troopers go through extensive training in exotic locations. Their equipment is also much more expensive than standard trooper equipment. Their helmets have more sophisticated sensors and their armor is coated with materials that make them harder to detect by enemy sensors. Each Death Trooper also goes through secret medical procedures to make them faster, stronger and probably smarter than a standard human. All this extra expense means the Empire would limit their number, the same way Vader's TIE was never mass produced because the hyperdrive and shields made it too expensive.
All this information is taken from The Rogue One Ultimate Visual Guide.