for ( @array1 ) {
  my ($id,$name,$ref) = split /,/;
  # You may wish to add some error checking to make sure the
  # hash key $id does not already exist
  $keyhash{$id} = { NAME => $name,
		    REF  => $ref,
		    MANY => [],
                  }
}

for ( @array2 ) {
  my ($id,$name,$ref) = split /,/;
  # Warn and do nothing if a record is found for which the
  # $id is not already in %keyhash
  unless ( defined( $keyhash{$id} ) ) {
    warn "No such record $id!\n";
    next;
  }
  push @{$keyhash{$id}{MANY}}, [ $name, $ref ];
}