Isso é bem simples com o bash. Basta iterar os arquivos, extrair o ano, mês e dia e, em seguida, movê-lo de acordo.
#!/usr/bin/env bash
# iterate all the wav-files that has at least 3 dots in addition to the extension
for file in *.*.*.*.wav; do
# In the case of no files matching the glob, file will contain the glob itself
# which will make the mkdir later on create './*/*/*'. Avoid that by testing
# if file contains an existing file.
[[ -e $file ]] || continue
# split out year month and day from the filename
IFS=. read -r year month day _ <<< "$file"
# make sure the directories exist, then move it
mkdir -p "./$year/$month/$day" &&
mv "./$file" "./$year/$month/$day"
done