Hmmm... When someone has a moment please...

You can check Planetary happines by going to your planetary item screen and clicking on the races tab. "Shits" don't go rogue because of planetary happiness. Someone is running intelligence against you. I don't know about the crew problem.
I hope the queen can forgive my french...

~Slimbo

Everything that has transpired has done so according to my design...

Version 1.67:
11. Changed - When repairs on a ship are complete, its crew is restored to maximum.

SpaceEmpires.net | Space Empires Wiki

-----
"Good morning, Pooh Bear," said Eeyore gloomily. "If it /is/ a good morning," he said. "Which I doubt," said he.

Or the alternitive.
Send in the Space Marines!

Er, I mean, try to catch them with a fast ship (cruiser or smaler with max engines) with boarding parties and engine/weapon disabling weapons.
Just keep said ships parked someplace where they die rather quickly should the boarding ship be the one that tries to run off.

Alternitively, have ships travel in teams of at least two. If one goes rogue, go shoot the traitorous little mutineers with the other ship. If you loose your ship, the ship they get will at least not be in good shape and while likely be easy to catch with your other ships.

But then again, that's just me, I'd rather loose a ship (or two) than let the enemy get one of my ships.

A better solution is to have enough intel to stonewall intel efforts. If you have more intel you can completely halt their efforts by concentrating it on defense.