I hope what follows is what you are looking for. I searched CPAN for utility modules to deal with nested hash structures, and came up empty--perhaps my search skills are just not up to it. Anyway, I have two utility functions. One flattens out a tree--for instance, your $sysmon_data[0] comes out like this:

(
   ['metadata_cache_mgmt', 'max_open_databases', 'count', value],
   ['cache_mgmt', 'spinlock_contention', 'per_sec', value]
)
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where the values are what you get from looking up that series of keys. The other reapplies the keys to a (potentially initially undefined) hashref and returns a reference to the node found/created.

#!/usr/bin/perl
use warnings;
use strict;

# takes ref to zero-or-more levels deep nested hash structure
# returns list of array refs for each leaf containing, top down, the k
+eys
# to reach the node followed by the leaf value

sub leaves {
    my $node = shift;
    if (ref $node eq 'HASH') {
        my @leaves;
        for my $key (keys %$node) {
        push @leaves, map [$key, @$_], leaves($node->{$key});
        }
        @leaves;
    } else {
        [$node];
    }
}

# takes ref to nested hash structure and list of top-down keys to trav
+erse
# returns reference to to desired node

sub find_node_ref {
    my $noderef = \$_[0];
    shift;
    $noderef = \($$noderef->{$_}) for @_;
    $noderef;
}

our @in;
our $out;
$in[0]{foo}{bar}{baz} = 'bag';
$in[0]{foo}{fuw} = 'fu';
$in[1]{foo}{gar} = 'weeble';
$in[2]{foo}{bar}{baz} = 'bog';

for (my $idx = 0; $idx < @in; ++$idx) {
    next if not defined $in[$idx];
    for my $leaf (leaves($in[$idx])) {
        my $value = pop @$leaf;
        my $node = find_node_ref($out, @$leaf);
        $$node = [] unless defined $$node;
        $$node->[$idx] = $value;
    }
}

use Data::Dumper;
print Dumper \@in;
print Dumper $out;
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Note that some error checking would be good. If you have a structure like:

$sysmon_data[0]->{cache_mgmt} = 0;
$sysmon_data[0]->{cache_mgmt}{spinlock_contention} = 'foo';
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you will end up trying to use a node in $out as an array ref after setting it to a numeric value, resulting in an error. A given sequence of keys should either always or never be a leaf node.