n=0; for dir in ./*/; do
  [[ -d "$dir" ]] || continue 
  n=0
  for f in "$dir"/*; do
    [[ -f "$f" ]] || continue  
    d="$dir/subdir$((n / 1000))"
    mkdir -p "$d"
    mv -- "$f" "$d/"
    ((n++))
  done
done