All DLC for one game shares the same ID. So, different DLC for the same game has to be packed into one CIA, since you can only have one DLC CIA installed at a time. It can't to my knowledge patch the executable -- the game has to already be aware of the DLC and check for it. What happens after that is up to the game I suppose. Whether it imports game data directly from the DLC (so it works more like an update), or it simply checks for a flag to enable DLC that already exists either in the ROM or in an update. Whether it can replace files or not is probably down to how the game handles it.