Morale/happiness already is tied to taxes: more taxes = more unhappiness. So, in essence, getting more happiness means you can tax higher.
Happiness of planets should probably NEVER impact ships. Overall happiness of the empire, yeah, maybe, but it would a PITA to try and compute happiness of ships that weren't in a specific planet's orbit. And, logically, why should the happiness of a planet I'm within influence radius of have any bearing on whether that ship flips/goes pirate/etc.?