It depends on the scope of the decision that was made. Generally things like naming conventions are going to be company-wide (or at least language-wide if you use multiple languages), and should therefore be stored in company-wide documentation.
High-level design decisions, even if made after the formal design phase, should be documented alongside the usual design documentation.
Low-level coding decisions (such as choosing a linked list over an array) can be left in code documentation, unless it's a significant low-level decision.
Format of data can be low-level, high-level, company-wide or even extra-company in scope. It depends on what the data is for. If it's just a log file format, leave it in the code. If it's a company-mandated format, document it at that level.
The bottom line is document decisions at the highest level where they are appropriate, but not higher.