I have done the following to replicate this issue:
1. Obtain an Alakazam with Psyshock + Psychium Z. Max IVs, 0 EVs, and Serious Nature
2. Set up an NPC with a Chansey with no held item. Max IVs, 252 HP, 252 Defense, and Serious nature.
3. Used Psyshock on Chansey - The expected range of damage is ( 34.2 - 40.4%). I repeated this 10 times, and the average damage was ~37%
4. Use Z-Psyshock on Chansey - The expected range of damage is (30.3 - 35.9%) since it should turn into a special move that hits on the special side. I repeated this 10 times, and the average damage was ~75%
Given that Psyshock has 80 base power while Z-Psyshock has 160, it does indeed seem to be that Z-Psyshock is hitting the physical defensive side rather than the specially defensive side.
Thank you for reporting this, I have forward it to the internal tracker.