You need two passes, one to build a list of sub-keys, and a second to print the table. Consider:

use strict;

my %hash = (
    Downtown_Market => {Fruit => 1, More_fruit => 2, Even_more_fruit =
+> 3},
    Uptown_market => {More_fruit => 4, Fruit => 5},
    East_market => {Even_more_fruit => 6},
    );
my %columnLookup;
my @columns;
my $maxKeyLen = 0;

# Build list of sub-keys
for my $key (keys %hash) {
    $maxKeyLen = length $key if length $key > $maxKeyLen;
    
    for my $subKey (keys %{$hash{$key}}) {
        next if exists $columnLookup{$subKey};
        $columnLookup{$subKey} = @columns;
        push @columns, $subKey;
    }
}

# Print the table
for my $key (sort keys %hash) {
    printf "%-*s (", $maxKeyLen + 2, "$key :";
    print join ', ',
        map {exists $hash{$key}{$_} ? $_ : ' ' x length $_} @columns;
    print ")\n";
}
[download]

Prints:

Downtown_Market : (Even_more_fruit, More_fruit, Fruit)
East_market :     (Even_more_fruit,           ,      )
Uptown_market :   (               , More_fruit, Fruit)
[download]