What is the hidden meaning of "mi mi", the Chinese word for secret?
You're reading too much into it. The only clue to this meaning in the original characters has now been lost.
You can take a look at the following dictionary excerpt to see exactly what information has vanished:
Outlier:

COMPONENTS
禾
In 秘, 禾 is an empty component. It is a corruption of 礻. The original character was 祕 “god; deity,” from which the meanings “secret, covert, undisclosed” are derived.

密 is a phonetic loan if anything, where it contains the idea of &quot;secret.&quot;