Why are you not wearing a uniform today? is more natural.
Uniform requires... something else. "a uniform," "your uniform," or "the uniform" would all work; "your uniform" is probably the most common.
Yep, I agree. Unless you were to say “Why are you not in uniform today” but that’s a rather loose translation of “memakai seragam”. Like you, I reckon “your” is probably best.
I would ask this as, “Why aren’t you wearing a uniform today?”