HSMC 160 vs 180 pins?

The HSMC connector is not actually a standard part number.

Samtec produce the QTH series of connectors such as the QTH-090-04-L-D-A which is what is used on the Cypress board. Additionally they produce the "ASP-122952-01" which is an "Application Specific Part", which is the HSMC connector used by Altera for their boards.

These two connectors are very similar to each other, the ASP part is in fact a modified version of the QTH series in which the first bank (Bank 1 or A) is modified to remove every third pin on each side. You will notice if you look at the HSMC connector that on one bank it is missing some pins. This is done to allow high speed (10Gbps+) transceiver signals to be sent through the connector without experiencing a massive impedance mismatch.

However as these parts are essentially custom order, you have to purchase them direct from Samtec with an associate lead time (granted Samtec are very good as supplying connectors quickly), but also at increased cost. On the other hand you can buy the QTH series connectors directly from distributers like Digikey at lower cost as they are off the shelf. Cypress have used the 180 pin QTH connector on their board instead of the 160 pin HSMC connector, I presume for this reason.

The good think is that the two connectors are fully compatible. You can plug a QTH connector into an HSMC socket and vice versa without any mechanical issue. For boards which are not making use of the very high speed transceiver channels, and so long as the missing pins are not used, there is no electrical issue either.

I have in fact used the QTH connector on a daughter board recently due to availability and had no problems at all.

TL;DR; HSMC is a 160pin variant of the QTH series connectors which are normally 180pin. Interestingly actually there are actually 172pin on the HSMC and 192pin on the QTH because the three ground bars in the centre of the connectors each solder to the PCB in 4 places, so there are 12 extra ground pins on the footprint.