There is no problem. And is better this way. If one of that "3" banner get damage, you can still using the other two. There's nothing wrong on that.
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Also, what's happen with homebrew TID?
Most of them are identical and we can only identify by filename.
I will try to explain my point in a bit more detail and deal with the homebrew too.
For each unique game, there is 1 unique bannericon.bin
Each unique game, can be stored in many different formats and places (like on flashcard, as a real cart in slot1 or on the 3ds sdcard)
My suggestion is for the bannericon.bin to be stored only once, and be used by all /formats of the game.
Why?
Because it saves space on the 3ds SD card, and as a result wear and tear because fewer files are written and read
It saves time because twloader doesn't have to go through the process of creating a new, identical, banner file for each format of the game it runs into
If a bannericon is corrupted it needs to be repaired (even if you have 3 with different names a the corrupted one won't fall back to one of the others)
When it comes to titles sharing the same TID, which is indeed often the case with homebrew.
When we run into a shared TID we can use the internal name instead, or if that also fails the filename