Your NAND has been used with old Dolphin versions, right? The bad news is that it's a bit broken...
* There is an extra file in /sys that should not be here. Delete /sys/replace.
* In your NAND, it looks like some game/title .app files that should be in /shared1 (we call these shared contents) may have been installed as private contents (in /title/XXXXXXXX/XXXXXXXX). You have a surprisingly low amount of shared contents. This is a problem, as the system menu can get confused by the extra files being in the private title directory.
* No DLC is installed correctly. I guess you used Dolphin's Install WAD feature before ~5.0-3000? Under a title directory (/title/XXXXXXXX/XXXXXXXX), there are supposed to be exactly two directories: one called "content" (for private contents) and the other called "data" (for save data). All of your DLC titles (under /title/00010005) are missing the data directory. This is known to cause the system menu to do invalid reads and possibly crash.
* There's no system title, apart from the System Menu. In particular, you have exactly 0 IOS. This could cause issues too.
* There is an extra file in /sys that should not be here. Delete /sys/replace.
* In your NAND, it looks like some game/title .app files that should be in /shared1 (we call these shared contents) may have been installed as private contents (in /title/XXXXXXXX/XXXXXXXX). You have a surprisingly low amount of shared contents. This is a problem, as the system menu can get confused by the extra files being in the private title directory.
* No DLC is installed correctly. I guess you used Dolphin's Install WAD feature before ~5.0-3000? Under a title directory (/title/XXXXXXXX/XXXXXXXX), there are supposed to be exactly two directories: one called "content" (for private contents) and the other called "data" (for save data). All of your DLC titles (under /title/00010005) are missing the data directory. This is known to cause the system menu to do invalid reads and possibly crash.
* There's no system title, apart from the System Menu. In particular, you have exactly 0 IOS. This could cause issues too.