You can use
GCMM to extract the content of your real memory card.
You can extract it as full Raw dump, or game by game in .gci format.
• Method1
Rename the full memory card dump create by GCMM as .raw and put it in your /saves/ folder.
If using this raw dump doesn't work, follow method2.
• Method2
For this method, you need an existing memory card image created by Nintendont. Launch the game you want to play at least one time with "Memory Card Emulation" option enabled.
Then use Dolphin emulator's Memory card manager to move the savegame you want from your GCMM raw dump or from a .gci file into the Nintendont memory card.
Converting savegames format between DIOS MIOS and Nintendont
nmm to gci :
nmm2gci v0.3 by Suloku
gci to nmm :
gci2nmm v0.1 by Crediar.
https://gbatemp.net/threads/nintendont.349258/
Just tested USB Loader GX r1253. Works flawlessly with newer versions of Nintendont.