There are a couple of different things in Black Mesa that play sounds- the ones you seem interested in are ambient_generic entities, which play specific sound effects at specific times (including music tracks) and soundscape entities which play general background noises (like clanks and rumbles underground, distant gunfire topside, and sloshing water in flooded rooms) that don’t have one specific cue. Both reference outside sound files- if you change the files in question, every instance of the old sound will (in theory- see below) be replaced with the new one.
Ambient_generics reference an actual .wav file, by name. Since most music tracks are played in only one place, you can just name your new music to the old name and it will (hopefully) replace the music that plays without having to touch any of the maps. Given that there are a few people who have released soundtrack mods as is, this seems to work. However, if you wanted to create new music that plays where nothing played before, you would indeed need to edit the maps.
Soundscapes are more complicated. They too reference files that tell them what to play, but these are text-based and written in an odd sort of scripting language- it’s not hard to learn, but Black Mesa is terribly buggy about accepting modded content that uses these scripts. In theory if you changed one of the scripts the background noise in certain areas would change, but be aware that a lot of different places have the same soundscript referenced and changing one may change other areas you don’t expect. If you wanted to change the soundscape in one specific area to something else without affecting others, or wanted to add subsections of completely new background noises, you would need to alter the maps themselves.