I see that Engineer brigades get officers with xeno bonus... Does it means that adding these brigades on the surface of a planet with a ruin will help the xeno team?
No, the officer's Xeno bonus reduces the time that the brigade requires to recover ruins, which happens after the Xeno team has identified them. Edit: The combined Xeno bonus of the team members determines how quickly they do that.
Just to confirm, Sorium harvesters convert it automatically to fuel that goes into their fuel tank, right?
Correct.
Plus, mining ships can't work with cargo, I need to create an empty colony at the asteroid to have the minerals dumped there, no other mean?
Yes, you need a colony, empty or not, for the minerals. You can then use freighters or mass drivers to move the minerals. Edit: Though you could put cargo holds on the miner and have it load from the colony and them transport the mineral somewhere.