snes9xgit/snes9x — comment on commit 8db1c467ac7ada2d27584da1b72d9efcd5458f4c
File:  line 0
By BearOso:

What you're describing is impossible. The resampler changes occur after the channels have been mixed, which occurs earlier in the DSP. There's no way it could completely remove a sound effect like that.
Give it a try on bsnes and see if you can hear it there. I still notice in level 1-1 that the bird noises will overwrite the effect, which coincides with my suggestion that the level background music prevents it from playing.
If you're still insistent, I'll look for my cartridge and test it on the SNES to see if it's there.