FPGA to HPS interrupts

That connection to nowhere is a red herring, it really is connected. The reason why some of those other ports connect to blocks is for other reasons which would take too long to explain (and you don't need to care :))

One thing to be aware of is that those 64 interrupts from the FPGA can be level or edge sensitive so I would make sure the interrupt setting matches what your hardware provides, for example if your hardware provides an interrupt pulse but the GIC in the HPS is setup for level sensitive interrupts then the interrupt will be missed.