For the inner loop you can use an anonymous hash like:

while ($line = <FH>) {
    chomp $line;
    next if $line =~ /^$/;
    next if $line =~ /[#{}]/;
    $line =~ /^\s*(\S+)\s*(\S+)/;
    # new portion
    $host[$counter]{$1} = {$2};
}
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You could push or simply use a counter (which keeps the code cleaner). Just one idea anyway :).