I have both Densetsu and Dracula variants on the NES set and they also appear when searching with Explore. So they are not really handled differently, there is probably something else going on. But both are imported with the automatic Scan functionality, not Manual.
If I had a guess, you have imported both games at a different day, with a specific setting not set the same. And its when you import manually, you can select “System Name”. Make sure both entries have the same System Name applied to it, which also determines which database to use. You can actually see which database is assigned to it by going into the game entry in the Playlist > Akumajou Dracula (Japan) > Information > Database Entry. If there is no Database Entry, then its unknown to RetroArch.
You can also open the playlist file on the drive and search for the entry manually to see what db_name
is assigned to it. Lookup in your RetroArch directory > playlists > Nintendo - Nintendo Entertainment System.lpl and open it in an editor and then search for these entries. In example its this one for me:
{
"path": "/home/tuncay/Emulation/Roms/nes/nes_nointro/Akumajou Dracula (Japan).nes",
"label": "Akumajou Dracula (Japan)",
"core_path": "DETECT",
"core_name": "DETECT",
"crc32": "04379750|crc",
"db_name": "Nintendo - Nintendo Entertainment System.lpl"
},