For many disc based games like saturn,dreamcast,ps1 u can use a program called cdhman to convert all the individual .bin/,cue/track files into a single .cdh file and it really cleans things up.
https://archive.org/details/chdman
download the zip and place the .exe and .bat file together into the same folder has the game files and run the .bat file and it will convert them all to the .cdh that most emulators seems to use and it also will not mess with the original files if you still want to keep them around for whatever reason.
also for multidisc ps1 games using a tool called PSX2PSP can convert multi disc ps1 games to the PSP .pbp format for a single file for all disc. Duckstation can use these files not sure of all ps1 emus though.
I was also setting up LBAndroid on my pocket 2+ that came in and had this same problem with dreamcast and after finding and doing this it was great plus cleaned up my desktop rom files at the same time!
Hope this helps!