$project{$activeProject}{components}{"Software"}{subComponents}{"Database"}{label} is syntactically equivalent to $project{$activeProject}->{components}->{"Software"}->{subComponents}->{"Database"}->{label}.

The $project hash's values are hashrefs. You can modify the values of those hashrefs within a subroutine.

my %h;
$h{a}{b}{c} = 'd';

print "$h{a}{b}{c}\n";
f($h{a}{b});
print "$h{a}{b}{c}\n";

sub f {
  my $x = shift;
  $x->{c} = 'e';
}
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produces

d
e
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