That is valid XML for a node with no content or attributes.

#!/usr/bin/perl
use strict;
use warnings;
use feature 'say';
use Mojo::DOM;

my $xml = '<header>
   <id x_id="1">
      <a></a>
      <b></b>
      <c>NA</c>
   </id>
</header>';

my $dom = Mojo::DOM->new->xml(1)->parse( $xml );

say 'Current value of c: ' . $dom->at('id > c')->text;
say 'Please specify node c content: ';
chomp( my $node_c = <STDIN> );
$dom->at('id > c')->content( $node_c );
say $dom->content;
say 'add content to nodes a & b';
$dom->at('id > b')->content( 'Foo' );
$dom->at('id > a')->content( 'Bar' );
say $dom->content;
[download]

Output:

Current value of c: NA
Please specify node c content: 
derp
<header>
   <id x_id="1">
      <a />
      <b />
      <c>derp</c>
   </id>
</header>
add content to nodes a & b
<header>
   <id x_id="1">
      <a>Bar</a>
      <b>Foo</b>
      <c>derp</c>
   </id>
</header>
[download]