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The ONE Exception (When a Tree is Better)

You should use a dynamic file tree only if your office messaging system requires direct OS-level access via SMB/Network Shares.
For example, if your office wants to map the server as a network drive (Z:\) and browse files using Windows File Explorer, you must use a dynamic folder tree.
However, if users only access files through your app's web interface or mobile app, never use a dynamic tree. Keep it flat, use the database for organization, and let the app map the names virtually.
Final Verdict: Save everything to a flat folder with encoded names. Let your SQL database handle the "hierarchy" (folders, tags, dates, and senders). Databases are built for relational querying; filesystems are built for raw byte streaming. Use each for what they do best.