It sounds like you're automatically booting into your uneek emunand when the SD card is inserted. And it doesn't have DI - why there's no USB access.
Are you sure you set it up as uneek+di rather than uneek?
If that isn't it, I'm not sure what you mean by "register". A softmodded Wii doesn't have unified device drivers - please be specific about what software/loader/app is seeing the hard drive/sd or not for help with diagnosis.
The built EmuNAND is on the SSD. The "nands" folder on the root of the device contains a subfolder "pl_us," with the EmuNAND inside. There is also a "sneek" folder on the root of the SSD. containing the files di.bin, diconfig.bin, font.bin, kernel.bin, and nandcfg.bin
There's some other files on the SD card having to do with neek2o (armboot.bin in the bootmiineek folder, and kernel.bin in the sneek folder. bootmiineek and sneek folders are both on the root).
All of these files were copied directly from the ModMii "Copy_To_SD/HDD" folders, and have not been touched, rearranged, renamed, tampered, or otherwise interacted with from myself.
I am not booting into EmuNAND by default. In ModMii, I chose the option of Uneek+DI. I would have been happy to try and manually build a version of a Uneek+DI EmuNAND, but I couldn't find much consistently up to date information.
I have an "apps" folder on the roots of both devices (SD card and external SSD), with different homebrew applications.
When the Wii powers on, with both devices connected, it boots into the real NAND. On the real NAND, when I open the Homebrew Channel, it will only show the apps from my SD card, and none from the SSD. The only way I can get the SSD apps to show up is by ejecting the SD card.
From the home menu of the real NAND, I can use an installed channel to boot into the uneek EmuNAND.
From there, when I open the Homebrew Channel, I can see the apps from my SD card. If I remove my SD card like I do on the real NAND, no apps show up on the Homebrew Launcher from my connected SSD.
The issue in my original post, about the console freezing any time it has to restart while in the EmuNAND - such as exiting YAWMM or the Homebrew Channel, still applies.
My issues are: Not being able to access the "apps" folder from both devices at the same time in the Homebrew Channel on real NAND, not autobooting into EmuNAND, not being able to access apps whatsoever on EmuNAND from my SSD, and the freezing issue upon console restart in EmuNAND.
It's a black model "Family Edition" Wii, lacking all the GameCube controller/disc/memcard support.
I might try copying my own dumped and extracted NAND, but I'm not sure what other issues will arise from that. I think I'd only need to copy the sys.cert file, but I could be misremembering.
I hope this clarifies everything, and any help would be appreciated. Thank you.