Parsing of a compound noun with many words

The reason compound words (i.e. two or more words that act as one word part of speech) are hyphenated is for this specific reason, which is to avoid confusing the reader.

If it were written

threat-analysis model

There is no question that threat-analysis modifies model. If it were written

threat analysis-model

There would be no question that you are working with an analysis model of threats. If you are writing this, make sure you use hyphenation to make the meaning as clear as possible, and provide additional context in other sentences to bolster the intended meaning.

If you are supposed to glean understanding from a poorly written document lacking in context, I'd say try to ascertain the meaning by talking to the writers (if possible) or observe how others are interacting with the same document.

Words take their meaning from context. As "threat analysis" is a standard term in military intelligence my first guess would be that this a model pertaining to threat analysis. In other domains of discourse the meaning could vary.