You can get away with a higher sampling rate for your sound effects, but I've had trouble with using over 8-bit PCM@8000 hz for the opening 3DS bcwav. Maybe that's your problem?
Also, I've had trouble in the past getting it to work, even after using the correct file format. I believe it's best to use a theme that already has an opening sound effect. I've also had this problem with border graphics. Even after enabling the option in YATA's settings, it just doesn't work. So, I just use themes that already have them and replace the assets.
What file format are you converting from? Make sure it's mono, too. Also, as far as quality goes, it really helps to normalize your sound effects before you convert them to 8-bit WAV, or you'll get a noisy, low quality sound. An easy alternative would be to amplify the sound using Audacity.