I have your suggestion to improve your joke.
You could omit the word 'menstrual' as I doubt the average person would be able to tell the difference between menstrual blood and other forms of blood when it is raining on them from the sky unless they looked up and saw the source of the blood, in which case the joke would be:
How do you know when a witch is having a period?
You observe that she is bleeding from her vagina
(Agent Pr1ck llǝɯs ǝɥʇ sʇI ˙ǝɔɐld sᴉɥʇ ǝʇɐɥ l, Tue 11 Jan 2022, 1:54, 1 reply, 2 years ago)

Alternatively,
it could be that there are other telltale signs or foreknowledge of when her period is due. Hence:
How do you know when a witch is having a period?
She casts a spell on you because she's a bit short-tempered, and/or you know that her period is due and that she isn't pregnant.
(The Porcupine From Purgatory Writtern By the Winners, Wed 12 Jan 2022, 9:27, Reply)