Dual GPS Antenna Connection to Positioning Module
"Would having two antennas connected, one through PCB trace and other through direct SMA cable be a problem for the performance of the device?"
  


Absolutely. RF is a fickle creature and having stubs on a PCB is a good way of having neither antenna work.

However, all is not lost. The Hittite/ADI HMC849 is designed to switch between antennas and is not too expensive.  If you need it to automatically switch, try detecting any DC current to the external (active) antenna. More than about 2mA and you can safely say an external antenna is plugged in.