The only thing I can think of that is per se inefficient about multiple hashes is the need to have multiple references being passed around. The way I usually avoid this is simply a HoH:

$hash{ column_name1 }{ value1 } = value2;
$hash{ column_name2 }{ value2 } = value1;
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Update: Although, a more complex scenario might even require something like this to maintain a one-hash-for-all structure:

$hash{ DATA }{ table1 }{ column_name1 }{ value1 } = value2;
$hash{ DATA }{ table1 }{ column_name2 }{ value2 } = value1;
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