My former boat was a 34' CC ketch (Grampian 34), with a separate aft cabin. We had to walk through the cockpit. I suppose the major advantage was the huge storage space that wasn't taken up with a walk-through hall. As others have said, this arrangement also meant the cockpit did not have to be elevated.
Our boat came with an head in the aft cabin, but it was marginal so I removed it. While it was a bit of pain in the butt to have to go through the cockpit to get to the head, it really wasn't a big deal. It's a 34-foot boat, after all. At most, I had to walk 20 feet!
I'd want a walk-through on a larger boat, but on one this size, it would have meant a tremendous loss of storage space. I loved our completely separate aft cabin. It's the one thing I really miss compared to our larger 37' aft-cockpit cutter.