I’m not sure how many secrets are revealed in Scribal Secrets: Extraordinary Texts in the Torah and Their Implications by James S. Diamond (of blessed memory).
Indeed, the Torah has some textual abnormalities that are hard to explain, almost all dots above certain words. Diamond gives various explanations for them: the scribes are noting these words because they are in the wrong place, but they don’t want to remove them. Or we should pay close attention to this word because it has some importance.
Then there are large and small letters. In the Shema, it appears, this was done to highlight letters that could be easily confused and render the meaning heretical. Other small or large letters have no obvious meaning.
What fascinates me most are the inverted nuns in Numbers 10: 35-36. The author thinks that the nuns may indicate that this is an insertion from another source outside the Torah, the so-called Song of the Ark. We know that the Torah is a book built from various sources, but they were incorporated into the text without drawing attention to that fact.
If the inverted nuns truly act as quotes here, and they were once used more frequently in the Torah text for such interpolations, this is truly an amazing bit of Torah-lore.