For the purposes of abilities like Jess Pava, "when attacking or defending, you may re-roll one of your dice for each other friendly ship at range 1" does the ghost with the phantom docked count as one ship or two ships?

one

The Phantom and all its upgrades, effectively doesn't exist until it's deployed.

Docked ships aren't "ships" until they are deployed.

In Epic a Gonzanti could be carrying 4 fighters onboard but it is still only one ship until it deploys those fighters. The Ghost is thes same as is the Hound's Tooth.

A docked ship is explicitly ignored for all rules and upgrades EXCEPT the Title because it specifically calls out the docked ship.