Hello, I’m another user that’s had a softmodded Wii since the “Twilight Hack” days before the Homebrew Channel was a thing (you may or may not have seen me around on places like GBATemp under the name “Nintendo Maniac” which, fun fact, is was the “NM” of my username originates from).
Anyway, I too had major major issues getting USB flash drives to work and so, since I’m a PC hardware enthusiast that always gets all of my friends and family’s “hand me down”/other old PCs, I had a slew of 2.5" drives laying around. I figured that, if I could find a USB to 2.5" SATA adapter that worked then, in theory, I could use it with any 2.5" SATA drive which would also allow me to connect it directly via SATA, eSATA, or whatever future connector via an adapter (e.g. USB4).
I’ve been using the following vantec drive and I similarly recommended it to a family friend for it own Wii and Wii U systems, and it “just works”:
Protip, it’s only $7.99 at Microcenter and, if you’re a new customer, you can similarly get a free 240GB or 256GB SATA SSD (I believe it’s DRAM-less, but that’ll hardly matter for the Wii):
Also the aforementioned family friend runs a 2.5" mechanical hard drive with that Vantec USB adapter combined with a USB Y power cable. In my experience, it’s when using an SSD that, on a Wii U, does not require a USB Y power cable. However, using the very same 2.5" mechanical HDD on a Wii worked fine without the need for a USB Y power cable.
Lastly, you can actually have multiple partitions on a single drive and USB Loader GX will see both partitions, so you can have an NTFS drive for Wii games and a FAT32 drive for GameCube games. I think you might be able to use exFAT specifically for Nintendont as well, but don’t quote me on this as I have everything on a single FAT32 partition since the only Wii games I have that take up more than 4GB in wbfs format are Smash Bros Brawl, Metroid Prime Trilogy, and Metroid Other M (the latter of which I don’t own the disc for but rather my friend’s father does… or at least did? said friend can’t find the disc anymore)
…also I find it interesting that you say “take advantage of Nkit on emulator” when Dolphin does not actually full support Nkit due to it causing various issues (the easy go-to example is that Super Paper Mario straight-up doesn’t work, though that’s obviously a Wii game), and even Nkit itself will be (if it hasn’t done so already) basically superseded it with the newer RVZ format as newer versions of Nkit will create RVZ instead.