Technically not possible, snes9xgx does not rely on HBC while running game and HBC does not modify the way emulators are running. Once a ROM is loaded into Wii RAM, devices are not acceeded anymore and the only thing running is the emulator code.
This "flickering" seems more related to random frameskipping: for example, if the emulator is not running perfectly in sync with video hardware, the previous frame can eventually be displayed twice successively from time to time. If for some reason, the same frame is always being dismissed (desync is a rather periodic thing normally) and it appears to be an important animated frame in game, flickering might appear. This can be pretty random though and effect could vary upon different playing sessions or emulator versions, but definitively not HBC versions.