When using Tapu Koko GX's "Aero Trail" Ability, can I choose to move zero energy cards and switch it with the Active Pokemon?
No, you may not. It says if you do move energy, and moving "zero energy" is not moving energy; therefore you do not get to switch Tapu Koko GX with your Active Pokemon.
Source: TPCi Rules Team (2017-07-06)

Relevant cards

Note: All applicable cards may not be listed below.
SM2_135
SM2_153
SM2_47
SMA_SV93
SMA_SV93