my %hashedPolys;
for ( 0 .. $#polys ) {
    push @{ $hashPolys{ xmin( $polys[ $#polys ] ) % 100 }{ ymin( $polys[ $#polys ) % 100 } }, pop @polys;
}
...
for my $point ( @points ) {
    for my $poly ( @{ $hashedPolys{ $point[0] % 100 }{ $point[ 1 ] % 100 } } ) {
        if( pointInPoly( $point, $poly ) ) {
            ## take whatever action is appropriate
        }
    }
}