……呢

Learners first see 呢 in 你呢 and translate it as 'what about you'. That is one job, but it is not the only job. After 怎么, 为什么, 谁, or 哪儿, 呢 adds a puzzled, open feeling. It does not mean 'what about' when it sits in that slot. In “您怎么还要找大白猫呢？” ── [《找“大白”》](/read/looking-for-big-white#s9), the speaker is not asking 'what about finding'. He is wondering why the old man keeps looking.

With 呢, the question sounds curious, puzzled, or gently probing. Without 呢, the same words can sound flat, impatient, or like an accusation. Use 呢 when you want to keep it friendly; drop it only when you really mean to press someone.

吗 turns a plain statement into a yes/no question, like 你忙吗. It cannot ride after a question word like 怎么. 呢 does not ask for a yes/no answer; it adds curiosity to a full question. So 他怎么还没来呢 is natural, but 他怎么还没来吗 is broken.