Here's another, untested, approach. I'm going to assume that $id, your first-level key, is supposed to be the primary index of the table. A hash implies uniqueness of the keys, otherwise you'd lose data.

The task is to produce a hash, %kol, which contains a table's primary index values as top-level keys, and a hash of each row's other field/value pairs at the second level.

That second-level hash will almost fall in our lap if we use fetchrow_hashref() to read the table. There will be no need to hardcode or independently determine the column names.

First, though, we need to find out what the primary key is. You've assumed it will be id, but lets generalize and make this thing work for any table with a primary index. I'll leave out the connection and all that other stuff, picking up at your # Method n comment.

# Method Z
my @key_columns = $dbh->primary_key( $catalog, $schema, $table);
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Instead of relying on a count while reading the table to limit the number, we'll tell the database to do it for us.Oops, misthunk, lets have no limits.

# my $limit = 6;
my $select = $dbh->prepare("select * from $table");# LIMIT $limit");
$select->execute();
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Now we loop through fetchrow_hashref to get a col/val hash of each row. For each, we'll delete the primary key columns, welding together their values to make a top-level key for %kol ( it may be a little unfamiliar to use delete that way, but it's a handy trick). What's left in the $row hashref is exactly what you want for the second-level hash, so we just plug that reference right in there.

while (my $row = $select->fetchrow_hashref()) {
    my $key = join '', delete @{$row}{@key_columns};
    $kol{$key} = $row;
}
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That's it! You may want to join the key elements using some unlikely character like "\0", just in case you want to extract them from the key later. We didn't need to call finish() on any handles because we didn't leave anything unread.

I have no idea how that will benchmark. It avoids a good bit of data copying, so it ought to be competitive.