OK, here's a standalone example that might help:

#!/usr/bin/perl

use strict;
use warnings;

use XML::LibXML;
use XML::LibXML::XPathContext;

my $parser = XML::LibXML->new();
my $doc    = $parser->parse_fh(\*DATA);

my $xc     = XML::LibXML::XPathContext->new( $doc->documentElement() )
+;
$xc->registerNs( xapi => 'xmlapi_1.0' );

foreach my $ccc ($xc->findnodes('//xapi:ccc')) {
    print "Found a ccc\n";
    foreach my $d2 ( $xc->findnodes('./xapi:d2', $ccc) ) {
        print "  d2 element contained: '" . $d2->to_literal . "'\n";
    }
    if(my $animal = $xc->findvalue('./xapi:zoo/xapi:critter', $ccc) ) 
+{
        print "  The mystery animal is '$animal'\n";
    }
}

exit;

__DATA__
<aaa xmlns="xmlapi_1.0">
  <bbb>
    <ccc>
      <d1>blah d1a</d1>
      <d2>blah d2a</d2>
      <d3>blah d3a</d3>
      <zoo>
        <critter>Monkey</critter>
      </zoo>
    </ccc>
    <ccc>
      <d1>blah d1b</d1>
      <d2>blah d2b</d2>
      <d3>blah d3b</d3>
      <zoo>
        <critter>Giraffe</critter>
      </zoo>
    </ccc>
  </bbb>
</aaa>
[download]

So the key point is that if you want to match an element that has a namespace (explicit via a prefix or inherited from a parent element) then you must include the namespace when you refer to the element in your XPath expression.

When matching a namespace, the only thing that matters is the URI. The prefix used in the source document (if there was one) is irrelevant. The prefix used in your code when you register the namespace URI is also irrelevant. What matters is that your XPath query includes a prefix that has been registered to associate it with the same URI as the namespace declared in the source document.

Thanks.
I had tried:
foreach my $d2 ( $ccc->findnodes('./xapi:d2') ) {
instead of:
foreach my $d2 ( $xc->findnodes('./xapi:d2', $ccc) ) {