Is it necessary to use 在？
Here's my explanation:
“你在做什么？” = “你正在做什么？”

在 can be normally used as abbreviation for 正在, which latter only means "right now". Therefore, 在 can be constitutive for the present continuous tense.

你做什么？could have different meanings or tense in different contexts, for example:
1. 你做什么（工作）？
2. 你（刚刚）做什么？
3. 你（这些天）做什么？
4. 你（打算）做什么？
5. 你（在）做什么？

When you add 在/正在, then You give a semantic restriction; the sentence can only mean: What are you doing? -- In this sense, it is necessary to add 在.