Hm. I think your routine is broken? I get these results:

c:\test>unionIntersect -N=10 -SHOW
2 2 3 4 5 5 8 9 12 14
4 4 7 7 9 9 10 10 11 11

barvin: 5 : 11
   buk: 2 : 11
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The union contains 11, and the intersection is only 2 (4,9) but your routine reports 5?

Anyway, this is my benchmark which shows a vec implementation is quite a bit faster:

#! perl -slw
use strict;
use Benchmark qw[ cmpthese ];

our $N ||= 100;
our $SHOW;

sub barvin {

        my ($in, $jn) = @_;

        my (%int, %uni);
        for my $i (@$in) {
                $uni{$i}++;
        }
        for my $j (@$jn) {
                $int{$j}++ if $uni{$j};
                $uni{$j}++;
        }
        print 'barvin: ', ((scalar keys %int), ' : ',  (scalar keys %u
+ni)) 
             if $SHOW;
        return ((scalar keys %int), (scalar keys %uni));
}

sub  buk{
    my( $aRef, $bRef ) = @_;
    my( $aBits, $bBits ) = ('') x 2;
    vec( $aBits, $_, 1 ) = 1 for @$aRef;
    vec( $bBits, $_, 1 ) = 1 for @$bRef;
    my $uCount = unpack '%32b*', ( $aBits | $bBits );
    my $iCount = unpack '%32b*', ( $aBits & $bBits );
    print 'buk: ', $iCount, ' : ', $uCount if $SHOW;
    return( $iCount, $uCount );
}

our @a = map int( rand $N * 1.5 ), 1 .. $N;
our @b = map int( rand $N * 1.5 ), 1 .. $N;

print "@{[ sort { $a <=> $b } @a ]}\n@{[ sort{ $a <=> $b } @b ]}\n" if
+ $SHOW;
cmpthese $SHOW ? 1 : -1, {
    barvin  => q[
        our( @a, @b );
        barvin( \@a, \@b );
    ],
    buk     => q[
        our( @a, @b );
        buk( \@a, \@b );
    ],
};

__END__
c:\test>unionIntersect -N=10
          Rate barvin    buk
barvin 33212/s     --   -29%
buk    47045/s    42%     --

c:\test>unionIntersect -N=100
         Rate barvin    buk
barvin 4111/s     --   -53%
buk    8777/s   113%     --

c:\test>unionIntersect -N=1000
        Rate barvin    buk
barvin 357/s     --   -64%
buk    998/s   179%     --
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