When using the counters from efficiency committee, it states you cant advance. But can shipment from sansan still place advancement counters on it?

Yeah, if it places advancement tokens instead of advancing, you can still place tokens on it.

At least that's what I'm assuming from the wording on SanSan. I'm not entirely sure.

That is correct. Spending an Efficiency Committee token means you can no longer take advancement actions but cards like Shipment from SanSan are perfectly valid.

Indeed there are HB decks based around that exact kind of thing to simply score out all the 2 for 3 agendas out of hand after scoring an Efficency Committee (and using HB's retrieval cards to fetch the shipments back if required).

Nice, thanks for the response