I had something similar on my 3ds too, but I fixed it by deleting all .cia I manually installed. Did you try deleting all custom .cia of things like NTR, freemultipatcher & even all .cia installers too. Also did you use FBI/devmenu to unistall them on both nand & emunand? It could also be a title.db/ticket.db issue if you injected a title.db/ticket.db into any of the nand but didn't have the app installed on the targeted nand , which is why I recommended to delete all manually installed .cia's. If reflashing a clean sysnand didn't solve
it, then your problem is related to your emunand or when reversed (reflashed emunand) you sysnand. I've had those black tiles more often after using FBI to install the apps on both nand & SD. In such a case I immediately deleted & reinstalled the apps & the black icons were gone. It happened the most to me when used FBI & devmenu in emunand to install things on nand.
Another fix might be to delete the title.db + import.db & make a file called title.db/import.db in your Nintendo dbs folder & then go to datamanagement on your device to unlock sd & rebuild your database (it'll remove all installed things you had so backup your Nintendo folder 1st so you can copy everything except title.db & import.db back Hope this help you fix it.Sorry if this doesn't help I consider myself still a noob afterall. xD
Btw did it happen to you with a linked emunand?I had a linked emunand if it helps solving it.