To get the counts, I had to iterate over the lines. There might be a better solution, I'm not a PDL expert. The resulting piddle has the count as the last element:

#!/usr/bin/perl
use warnings;
use strict;

use PDL;

my $p = pdl(
    [0, 1, 2],
    [3, 4, 5],
    [6, 7, 8],
    [0, 1, 2],
    [0, 1, 2],
    [6, 7, 8],
    [0, 1, 10]);

my $u = $p->uniqvec;

my @r;
for my $i (0 .. $u->dim(1) - 1) {
    my $vec = $u->slice(':', $i);
    my $matches = $p == $vec;
    push @r, [ $matches->andover->sum ];
}

print $u->glue(0, pdl(@r));
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[
 [ 0  1  2  3]
 [ 0  1 10  1]
 [ 3  4  5  1]
 [ 6  7  8  2]
]
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($q=q:Sq=~/;[c](.)(.)/;chr(-||-|5+lengthSq)`"S|oS2"`map{chr |+ord
}map{substrSq`S_+|`|}3E|-|`7**2-3:)=~y+S|`+$1,++print+eval$q,q,a,
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