Apologies for the thread necro, but I had a very similar incident yesterday.
I was using Snes9x*GX* and it froze on its pause menu. After rebooting the Wii, the (FAT32 32k) hard drive had been overwritten. There was a (new) single file with a non-roman single-character filename in the root of the drive. There was also still a nands folder, but not the one the drive started with - this one had almost nothing in it. Everything else that used to be on the drive was missing. The used/free space as read by Windows indicated the original files were still there/not deleted properly.
After putting the drive through Windows' built in repair, it found a malformed volume called StarOcean-something (the game that was running in Snes9xGX during the freeze). Basically, it looks like a problem with SNES9xGX can lead to catastrophic drive overwrites. I've found other threads hinting at the issue, they appear to blame libogc and/or power loss to the drive during Wii reboots (for drives like mine that are powered from the Wii).
I'm looking very askance at using these emulators anymore, I may switch to Retroarch plugins in Wiiflow for SNES and NES. FCEUGX and SNES9XGX both use the "standard" pause menu (does this come from libogc?) and both freeze on that pause menu fairly frequently. The chance they're also going to wipe my hard drive again is just not acceptable.