I think the use of the words “secret messages” in the OP is rather loaded towards Gnosticism…
The Protestant third rule of scripture interpretation is:
“If the Plain Text Makes Perfect Sense, Seek No Other Sense”
Contrast with the ancient Hebrew method: PRDS
P'shat (straight, direct, literal), Remez (hinted-at), D'rash (inquire, seek) and Sod (secret, mysterious).
Within this second view, deeper meanings never contradict the plain meaning.