It's looks like you've got at least five levels there, not three. First, here's a tip that will save you a few keystrokes. Once you're "in" a complex structure, you don't need to type the -> operator to dereference. So

$project{$activeProject}->{components}->{"Software"}->{subComponents}-
>{"Database"}->{label}
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can be written $project{$activeProject}{components}{Software}{subComponents}{Database}{label}

You were on track for adding elements to the hash without typing the entire structure each time. To add stuff to that final level, you can do:

$subDatabase->{label} = "whatever";
$subDatabase->{foobar} = "something else";
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Since $subDatabase is a reference to the original structure, the changes will persist after you leave the sub (assuming %project is defined outside the sub's scope, as it appears.)

Note: It's always a good idea, but especially when working with complex data structures, to turn strict and warnings on, if you haven't already.