Yeah, the FDS does have another sound channel (through the RAM cart's chipset).  Many games don't use it much though.  Metroid for example only used it on the title screen, some sound effects (door opening), when you pick an item up, and the end music.  Zelda used it for the title screen music and sword-throwing sound.  That Doki Doki Panic game used it for sound effects, and when they released it in the US as SMB2 it sounds like they converted and recorded the sounds into samples.

Most likely an emulation problem.  IIRC, Meridian Advance is pretty old, but I'd think FCEU would have good FDS sound emulation, but maybe not.  I dunno which other player would be the most accurate.