$_ ist the default variable for loops, you don't need a special inside variable.
If you got such a loop (and don't see any commands that could harm your computer), it's wise to

for (keys(%{$ini{$hostnames[$i]}})) {
 print "Slot: $_\n";
 push @slots,$_;
 print "IfIndex: ${$ini{$hostnames[$i]}}{$_}\n";
 push @ifindices,${$ini{$hostnames[$i]}}{$_};
}
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This will show you what is happening.

Let's split the lines: $hostname[$i] contains your hostname. This is used as a key for the %ini - hash. So we could simplify it for better understanding as

for (keys(%{$Hostpart_from_INI})) {
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$Hostpart_from_INI contains a reference to what Config::INI found for this hostname (the one for the current loop run). It is a Hash-Reference, so we could also write:

for (keys(%Host_Data_from_INI)) {
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Okay, now we're here with a simple Hash. Each loop run gets another key from the Hash %Host_Data_from_INI. If you got Problems with $_, we could add it:

for $_ (keys(%Host_Data_from_INI)) {
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You should try the following for better understanding:

perl -le 'for (1,2,3) { print $_; }'
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You could also add the $_ behind the for or you could use any other variable.
Still with me? Okay, let's write your loop using the simplified form:

for (keys(%Host_Data_from_INI)) {
 push @slots,$_;
 push @ifindices,$Host_Data_from_INI{$_};
}
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Remember: We changed nothing, the code is still the same. All we did was renaming things and solving references to show what Perl sees when executing the script.