You're going to run into problems with the second block of code you posted.

You treat $hash{$key1}{$key2} as having a scalar, string value (for use as a hash key):

my $key3 = $hash{$key1}{$key2};
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Then in the next line you treat the same value as a hash reference:

my $value = $hash{$key1}{$key2}{$key3};
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You are effectively working on two different data structures:

%hash = ( key1 => { key2 => $some_key } );
%hash = ( key1 => { key2 => { $some_key => $some_value } } );
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