I journal to create a concrete representation of my thoughts at a point in time. Writing with intent to explain to yourself forces a structured view on assumptions, deductions, inductions, etc. rather than having them bounce around in your head as a wobbly mass of jello.

The structuring of your thoughts and emotions, by nature, forces a certain amount of meta cognition and distance from your feelings as you can more easily identify and further think about the insights, inconsistencies, etc. You have a scaffolding that you can continue to build on or rebuild.

Beyond the immediate thinking, it's also interesting to see how the thoughts on something change over time or how they relate to other topics. Now, I'm thinking about my thinking rather than just focusing on the immediate topic.

Deep thinking without a sense of permanence can be great as a start of ideas. You need a low cost way for ideas to form where you can pick the most promising ones for more introspection. But without permanence, there's this danger that you get lost in your half-formed thoughts because it has a lot of "feel" in it and makes it hard to build on or critique. There's a danger that you end up going down an Escher staircase mentally and emotionally that seems like the logical, immediate thing to do but is a contradiction at a higher level.