First, a minor stylistic issue; the line

($limit < $default) ? $time_to_die = $limit : $time_to_die = $default;
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Is more often written

$time_to_die = ($limit < $default) ? $limit : $default;
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But back to the matter at hand. In general, any value that has to be looked up in a hash or through a function is going to be slower than just grabbing a scalar. A quick benchmark I wrote:

package Apache::Test;

use strict;
use Apache::Constants qw(:common);
use Benchmark;
use vars qw($r); # Not a good idea in general, but I couldn't
                 # figure out how to pass parameters in a
                 # benchmark.  Works fine for benchmarking purposes.

sub handler {
        $r = shift;

        $r->send_http_header;

        $r->print("by_dirconfig:",timestr(timeit(250000,\&by_dirconfig
+)),"\n");
        $r->print("by_var:", timestr(timeit(250000, \&by_var)), "\n");

        return OK;
}

sub by_dirconfig {
        my $time_to_die;

        if ($r->dir_config('TimeLimit')) {
                if ($r->dir_config('TimeLimit') < $r->dir_config('Defa
+ultLimit')) {
                        $time_to_die = $r->dir_config('TimeLimit');
                } else {
                        $time_to_die = $r->dir_config('DefaultLimit');
                }
        } else {
                $time_to_die = $r->dir_config('DefaultLimit');
        }
}

sub by_var {
        my ($default, $time_to_die, $limit);

        $default = $r->dir_config('DefaultLimit');
        $limit = $r->dir_config('TimeLimit') if ($r->dir_config('TimeL
+imit'));
        $time_to_die = ($limit < $default) ? $limit : $default;
}

1;
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Which leaves in my browser window:

by_dirconfig:14 wallclock secs (15.28 usr + 0.03 sys = 15.31 CPU)
by_var:11 wallclock secs (12.07 usr + 0.02 sys = 12.09 CPU)

Conclusions are about the same as yours, just thought I'd add my results.