I recommend Retroarch for those systems because it's just easier that way. You install the cores and set up hot keys once and you're done. RA and RP3+ will play all those systems just fine, you might just have to futz with the Daijisho path. It's when the systems get newer that the performance benefits of a stand alone emulator outweigh the RA convenience IMO.
Your SD card mount/path shouldn't change every time. But I don't take it out much - use FTP to transfer your ROMs.