Besides Data::Compare proposed by Eily, there are also Data::Walk and Data::Walker. When you put it together the problem seems to have a reasonably simple and neat solution:

use strict;
use warnings;

use Data::Walk;
use Data::Compare;

sub find_structure_part {
    my $search_space = shift;
    my $target = shift;
    my $found = 0;

    walk sub {
        if (not $found and Compare($_, $target)) { $found = 1 }
    }, $search_space;

    return $found;
}
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