Actually, it’s because those balls were specifically designed for certain types of trainers. As uncomfortable as it is to admit this, it’s largely due to business. Putting it another way, ultra balls are the best type of universal poké ball (meaning its capture rate is consistent in all situations, and it’s the best type of ball available to the public wherein that’s true), but it still has a reasonable chance of failing. Meanwhile, you have balls that work better than the ultra in certain situations, but in other situations, they’re comparable to poké balls. Additionally, these other balls can be marketed towards certain demographics. Dusk, for example, can be marketed towards those who specialize in cave or nocturnal pokémon, dive can be marketed towards fishermen and swimmers, timer can be marketed as a last-resort poké ball for trainers after specific pokémon, nest can be marketed towards those with exceptionally strong teams, and so forth.
By contrast, there is a poké ball that works better than ultra balls (the master ball, specifically), but this is not available to the public. The reason why is because if everyone has access to a ball that has a 100% capture rate all of the time, they’ll be less likely to buy balls because they’ll need far, far fewer of them.
In short, it’s not so much because of a technological restriction as it is because of capitalism, anonymous.
As for what would happen if a poké ball’s battery runs out, that’s extremely unlikely because of how long the lifespan of a ball’s power source actually is (and because various transfer systems also recharge said power source every time a ball is converted to electricity and data), but should it happen, there’s a failsafe within the ball that will automatically release your pokémon just before the battery dies. It’s the same failsafe that’s triggered whenever your poké ball becomes too damaged to safely contain a pokémon.
The Pokédex According to Bill 