If parts of your application (DB, EXEs, etc.) are taking seconds or milliseconds to run, spending time optimising map to save a few micro- or nanoseconds is unlikely to be worth the effort.

Another consideration is whether this is a short-lived application that's run multiple times or a long-lived application that's run with multiple iterations.

There are some JIT (just-in-time) possibilities that may be worth consideration. If you end up with a lot of get_X_for_Y() subs, and some are only called infrequently, you can create mappings just when they're needed; something like this using state (which requires v5.10):

{
    my %dat_by_id = ...;

    sub get_X_for_Y {
        my ($Y) = @_;
        state $map_Y_to_id = {
            map +($_->{Y} => $_->{id}), values %dat_by_id
        };
        return $dat_by_id{$map_Y_to_id->{$Y}}{X};
    }

    sub get_X_for_Z { ... }
    sub get_V_for_W { ... }
    ...
}
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Note that the anonymous block gives %dat_by_id lexical scope such that it is only visible to the subs; while the subs themselves are visible to, and accessible from, the entire script. This prevents inadvertent changes to %dat_by_id which could introduce bugs which are hard to track down.

Also note that the placement of the above code within your script would be important. The assignment to %dat_by_id should occur before any calls to get_?_for_?() are made. An alternative to this would be to use some combination of BEGIN, INIT, etc. blocks; I don't know enough about your code to comment further on this; see perlmod: BEGIN, UNITCHECK, CHECK, INIT and END for more about these. There would, no doubt, be other ways to handle this but, as previously stated, I don't know enough about your code to offer further advice.