There is no problem with pins H38 and H39 not being connected to GND on the Arria® V GX FPGA Development kit populated with the 5AGXFB3HF40 device. According to the Quartus® II Pin Planner and Pin-Out file for this device, pins H38 and H39 should be connected to GND.
The 5AGXFB3HF40 device does not support the HSSI channel on pins H38 and H39 which are supported in different densities of Arria V devices in this package option. They are shown as GND connections for the 5AGXFB3HF40 device to support device migration with the 5AGXFB3HF40 and 5AGXFB7KF40 devices. The reason why H38 and H39 are shown as GND pins is to prevent those pins from floating when using device migration.