If you have a crew (like jan ors) equipped on the phantom, can you use its effects while its docked with the ghost?

No. Neither the upgrades nor the pilot ability of a docked ship have any effect; they're not in play until the ship is deployed. (The effect of the Phantom title is a specific exception to the general rule.)

I thought Wingman would be fantastic on the Phantom, then I read the rules that docked ships are inert until they are deployed.

ok, thanks