In No$gba, go to Options->Emulation Setup and in NDS Backup Media, choose EEPROM 0.5KB. Then go to File->Reset (you can save the the settings if you intend to play later Options->Save options).
(In iDeaS, go to Options->EEPROM 4Kb and load your rom afterwards).--->does not work actually.
On DeSmuMe, the save type should be detected automatically but not sure whether the game is compatible.