Why did Arishem design Makkari to be deaf?
A semi-canon explanation is that the being deaf prevent Makkari to withstand the sonic booms she creates from her superspeed. But why could't Arishem design her to use a superspeed without being deaf?
Now, first it's important to understand Arishem's goal - to birth Celestials. He's a powerful being, but he's not a "perfect designer" or "God" as humans tend to refer too.
Arishem is actually pretty human in his trial-by-error approach, that he keeps doubling down on his error and fix them as they come along.
First he make Deviants to eat predators -> Oops, Deviants evolve to eat humans -> Create Eternals that can't evolve -> Oops Eternals instead develop emotions and personality
This is similar to so many things humans do in real life: E.g. Pest beetles in Australia -> They bring in cane toads --> Cane toads become new invasive species, destroying local fauna -> now offers bounties to catch and kill cane toads.
Arishem just wanted someone with superspeed, so he just made that person deaf to use that power. He probably didn't think of it as a disability of inconvenience to Makkari, he just wanted a superspeed soldier. Or even care at all.
Same with Sprite, he just wanted an illusionist without considering the pain and struggle she will face as a kid that doesn't age.
There was a good line by Sprite "why did Arishem made me this way?" The answer is no one knows, probably Arishem doesn't even know himself and neither does he care. However, if somehow being deaf or being a kid prevented the goal of birthing a Celestial, Arishem might do somethng to "fix" this in the next generation of Eternals - who knows, maybe make them full androids?
And as real life analogy, I'm sure this same question would have crossed the mind of anyone who is struggling with something that the greater society frowns on. To add a religious aspect, we can even add "How do you know that being made is not part of (insert deity)'s grand design? We cannot understand (insert deity)'s plans, we just have to trust in (insert deity)'