I want to expand this to include AM/PM indicators, but I'm not sure if it'll be possible.
In addition, I would like this to work across all applets, but that will take some time to flesh out.
Required Reading
The 3DS uses the 24-hour time format to display the time on the HOME Menu among other applets. This guide shows you how to convert the 3DS system's clock on the HUD of the HOME Menu to a 12-hour format.
This will not affect other applets such as System Settings or the Nintendo eShop at the moment, meaning you will only see a 12-hour clock on the HOME Menu.
The clock will display in Japanese 12-hour time, which means that 12:00 (both midnight and noon) will be displayed as 0:00. All other hours of the day function as expected.
A computer running Windows, or Wine for Mac/Linux (Required to run MSBT Editor)
Instructions
In this guide, <Your language> is to be substituted with your consoles language selection. For example, US_English.
Section I: Prep Work
Extract Home Menu Rebuilding Tool as well as MSBT Editor Reloaded to a new folder on your computer
Press and hold Start, and while holding Start, power on your console. This will launch GodMode9
Press HOME to bring up the action menu
Select "Title manager"
Select "[1:] NAND / TWL"
Scroll down through the list and select a title labeled (CTR-N-HMME). This is the HOME Menu application
Select "Manage Title..."
Select "Build CIA (standard)"
Push A once it is finished
Push R+Start to power off the console
Insert the SD Card into your computer
Backup the .cia file in the gm9/out folder to a safe place on your computer. It ends with (CTR-N-HMME).standard.cia
Make another copy of this .cia file in the folder created in step 1
Rename it to HomeMenu.cia
Copy HomeMenu.cia to the Home Menu Rebuilding Tool folder
Section II - Modifying
Open HMRT.bat
Push 1 on your keyboard to extract the components of the Home Menu
Push 5 on your keyboard to decompress the components
Keep the window open and open MsbtEditor.exe
Drag the file named hud_msbt.LZ from ExtractedRomFS/message_hud/<Your language> into MsbtEditor
Scroll down and select lau_hours in the list on the left
Change %H to %h in the first text box labeled "Edit:"
Push Ctrl+S to save, then close MsbtEditor
Section III - Installing
The file structure for a US_English 12-hour time patch file.
In the Home Menu Rebuilding Tool window, push 6 on your keyboard to recompress the components
Close the Home Menu Rebuilding Tool window.
On your 3ds SD Card, create the following folder corresponding to your region:
JPN: luma/titles/0004003000008202/romfs
USA: luma/titles/0004003000008F02/romfs
EUR: luma/titles/0004003000009802/romfs
CHN: luma/titles/000400300000A102/romfs
KOR: luma/titles/000400300000A902/romfs
TWN: luma/titles/000400300000B102/romfs
Create the message_hud/<Your language> folder inside the romfs folder.
Copy hud_msbt_LZ.bin from ExtractedRomFS/message_hud/<Your language> to the new folder.
Eject your SD Card and put it back in the console.
Start your device and hold SELECT to enter the Luma3DS configuration screen
Press (A) on ( ) Enable game patching to tick it (if it is not already ticked) (x)
Press START to boot the the HOME Menu
The HOME Menu's clock should now be displaying 12-hour time.
Read this box closely!
This method is much less preferred than LayeredFS, as it makes direct edits to your system HOME Menu. Only use this as a last resort and if troubleshooting LayeredFS was not successful!
Create/update your NAND backup! When making changes to your device, there is always the chance you will brick.
Having a custom HOME Menu installed breaks system updates. If you want to update your system, you will have to restore your HOME Menu with a blank HomeMenu.cia first.
In the Home Menu Rebuilding Tool window, push 6 on your keyboard to recompress the components
In the Home Menu Rebuilding Tool window, push 2 on your keyboard to rebuild the HomeMenu CIA.
Copy the outputted HomeMenu_edited.cia file to the root of the SD card
Press and hold Start, and while holding Start, power on your console. This will launch GodMode9
Navigate to the [0:] SDCARD drive, then select the HomeMenu_edited.cia file
Select "CIA Image options..."
Select "Encrypt file (...)"
Select "Encrypt inplace"
After it is finished, push A to continue
Select the HomeMenu_edited.cia file again
Select "CIA Image options..."
Select "Install game image"
Press A to unlock SysNAND (lvl1) writing, then input the key combo given
Push A twice then Start to reboot
The HOME Menu's clock should now be displaying 12-hour time.
If the HOME menu does not boot or you encounter any other problem, it is recommended that you ask for help on the Nintendo Homebrew Discord server in one of the 3DS assistance channels, mentioning that you were following this guide.