According at wiring diagram listed on that page https://www.seeedstudio.com/WM1302-Pi-Hat-p-4897.html it looks like the GPS chipset is on the hat so antenna connector on hat is for GPS, the one on Lora board is for Lora antenna zhich makes sense 
According at wiring diagram listed on that page https://www.seeedstudio.com/WM1302-Pi-Hat-p-4897.html it looks like the GPS chipset is on the hat so antenna connector on hat is for GPS, the one on Lora board is for Lora antenna zhich makes sense