What is the grammatical construction of the clause "Emotions that Maria had thought were buried deep enough ..."

Solution 1:

This question has basically answered in the comments, so I will not explain in detail what has already been said.

The part in bold is indeed not a full sentence. It is an appositive which is normally marked by comma(s), but in literature, peculiar punctuation like this can be used. The apposition is a Noun Phrase consisting of the head Emotions and the relative that Maria had thought were buried deep enough so they could not betray her at the worst possible moment. It is this relative that seems to be confusing you.

1. Emotions = subject of the verb were buried
2. that Maria had thought were buried deep enough so they could not betray her at the worst possible moment. = relative clause, within which:

• [that they] were buried deep enough = direct object of had thought
• so [that] they could not betray her at the worst possible moment = consecutive adjunct establishing the effect of were buried deep enough.

So the object of had thought is not emotions but the object clause were buried deep enough which could be replaced by a non-finite infinitive clause:

Emotions that Maria had thought to be buried deep enough so they could not betray her at the worst possible moment.