I don’t know if this is a weird coincidence or a logical development, but 密 and 秘 have one more thing in common, apart from showing up together in 秘密 (himitsu: secret, to keep secret + secret) and sharing the 必 component. You can use them interchangeably when writing the following word:
hisoka: secret, private, surreptitious
In fact, these are all possible ways to represent hisoka in kanji:
密か 秘か 窃か
Same goes for the adverbial form: hisokani (inwardly, secretly).
But when it comes to writing kokoro hisokani (inwardly, secretly), it seems that only 心密かに will do.
The standard yomi for 秘 are HI and hi(meru), but Breen says that hiso(ka) and kaku(su) are also possibilities.
Henshall has quite a lot to say about the evolution of the third kanji here, 窃 (SETSU, nusu(mu), hiso(ka): to steal, stealthy). He even notes that “to steal” is the original meaning, whereas “stealthy” is an associated meaning, as in English. (Never thought about that before!)
This means there are two kanji that mean “to steal” and that have the kun-yomi of nusu(mu): 窃 and 盗. Curiouser and curiouser. But 窃 appears in very few words, most notably in 窃盗 (settō: theft, to steal + to steal). Furthermore, it appears that 窃 never stands alone. Even though the kun-yomi of nusu(mu) and hiso(ka) exist, they’re no longer used.