I think you will want to do this with a couple of passes.

In the first pass, read each ID, and keep track of how many columns each table has, as well as saving individual values per table.

In the second pass, for each ID, collect the corresponding values from each table, or assign the appropriate number of "n.a." (if the ID isn't defined for the table).

For example:

# Strict
use strict;
use warnings;

# Libraries
use Data::Dumper;

# User-defined                                                        
+       
# Define tables, each one a separate value in the hash "$ptables"
my $ptables = {
    'tab1' => [
        "ID column | column 1",
        "gene 1 | value 1.1",
        "gene 2 | value 2.1",
        "gene 4 | value 4.1",
        "gene 8 | value 8.1",
    ],
    'tab2' => [
        "ID column | column 1 | column2",
        "gene 1 | value 1.1 | value 1.2",
        "gene 3 | value 3.1 | value 3.2",
        "gene 4 | value 4.1 | value 4.2",
    ]
};

# Globals
my %output;
my %ncolumns;
my %values;
my @tables = (sort keys %$ptables);                 # Get all table na
+mes

# Main program

# First pass -- parse each table to fetch all the IDs
print "=== Pass 1 ===\n";

foreach my $table (@tables) {
    my $ptab = $ptables->{$table};                  # Assign to table
    my @rows = split(/\s*\|\s*/, shift @$ptab);     # Get column headi
+ngs
    shift @rows;                                    # Discard "ID colu
+mn"
    my $ncols = @rows;                              # Find number of c
+olumns
    $ncolumns{$table} = $ncols;                     # Save # of column
+s
    print "Reading $table; $ncols col(s)...\n";     # Announce table n
+ame
    foreach my $line (@$ptab) {
        my ($id,@vals) = split(/\s*\|\s*/, $line);  # Get ID and value
+s
        $output{$id} ||= [ ];                       # Placeholder for 
+ID
        $values{$table}{$id} = [ @vals ];           # Save values for 
+table/ID
    }
}

# Second pass -- process each ID, adding values from each table
my @ids = (sort keys %output);
print "=== Pass 2 ===\n";
foreach my $id (@ids) {
    print "Processing ID $id\n";
    my $pout = $output{$id};                        # Get current ID l
+ist
    foreach my $table (@tables) {
        my $ncols = $ncolumns{$table};              # Get number of co
+lumns
        my $pvalues = $values{$table}{$id};         # Get values for t
+able/ID
        if (defined($pvalues)) {
            push @$pout, @$pvalues;                 # Save values
        } else {
            push @$pout, ( "n.a." ) x $ncols;       # Missing value = 
+N/A
        }
    }
}

# Verify results
print "=== Verify results ===\n";
foreach my $id (@ids) {
    my $pvalues = $output{$id};
    printf "%12.12s | %s\n", $id, join(" | ", @$pvalues);
}
[download]

The output of which is:

      gene 1 | value 1.1 | value 1.1 | value 1.2
      gene 2 | value 2.1 | n.a. | n.a.
      gene 3 | n.a. | value 3.1 | value 3.2
      gene 4 | value 4.1 | value 4.1 | value 4.2
      gene 8 | value 8.1 | n.a. | n.a.
[download]

Of course, you can always add more tables to the master table $ptables.