Nope, it'll not fix in-game freezes. The fix for TWLMenu++ involved using the same SD argument passing system as nds-bootstrap (being IPC Sync).I was curious because I don't remember seeing this encrypted/decrypted thing back in the DS flashcards days.
Also, I would like to ask you about that progress bar lockups that was fixed in TwilightMenu, can it also help with in-game freezes? I had two freezes on the previous version that resulted in the 3DS not booting up unless if I reinserted the SD card. I haven't used TwilightMenu since then because I was worried about SD card damage.