First of all, don't modify the array over which for iterates.

If any part of LIST is an array, foreach will get very confused if you add or remove elements within the loop body

Fixed:

my @temp;
for my $h (@hosts) {
    if ($h =~ m/^\d{2}\z/) {
        for my $short (@shorts) {
            push @temp, "$short.area$h";
        }
    } else {
        push @temp, $h;
    }
}
@hosts = @temp;
[download]

The inner for loop can be replaced with map simply:

my @temp;
for my $h (@hosts) {
    if ($h =~ m/^\d{2}\z/) {
        push @temp, map "$_.area$h", @shorts;
    } else {
        push @temp, $h;
    }
}
@hosts = @temp;
[download]

You can also replace the exterior for loop with map too:

@hosts = map {
    if (/^\d{2}\z/) {
        my $h = $_;
        map "$_.area$h", @shorts
    } else {
        $_
    }
} @hosts
[download]

The above could be golfed, but I fear readability will suffer.

Filter isn't useful here since it only handles 1-to-1 transformations.