"Why not?"
Besides my Wii, I use the same external HDD to launch the games with XBMC (with Advance Launcher). Since I have everything organized in order to have each game displaying his cover, screenshot and tittle screen... it's convenient for me to have just only one file per game. Since I'm downloading/renaming hundreds of covers and screenshots, it makes things easier to be able to compare how many files I have in my "games" folder, and how many jpgs I have in the "covers" folder... that way I can know how many files I'm missing. I cannot do that if I have two files per game. Besides, I don't know if Dolphin supports split files.
I don't see why having an NTFS partition represents so much hassle to you. I have one FAT partition for Roms/DiosMios/Uneek/Homebrew, and one NTFS for USB Loading and WODE. Everything works great.
Also, I found NTFS much safer. FAT32 is not very reliable when you're pluging/unpluging your hard drive many times (my case), you can corrupt the whole partition by disconnecting without unmounting it first. I can't count how many times I got FAT drives corrupted that way. When I'm dealing with 1-2TB of worth data, I will go with NTFS.
For your game count, check you folder count in your wbfs folder, it resembles the amount of games
if you placed them with a proper manager.
Everything should be nicely organized folders, showing name and Title ID. You never have to look for anything.
If you would use proper managers/ backup loaders you should never have to compare your game/cover count.
You are doing things the hard way but, it seems you like it that way.
As for why you use NTFS for your Wii backup needs, still very shady.
But, seeing you have another use for the partition besides your Wii, it's understandable.
For the unmounting of your drive, again you do not make sense as for how this is NTFS related. Besides you mentioned you are using a dual setup fo you HDD.
Never disconnect any drive when it is is a write cycle.
This count for any format. Data might corrupt, not always noticable at first glance.
At least you now know the facts, you decide how you manage your media in the end.