If you include a fight, make the enemy hard to see and hit. And almost impossible to kill.

Because there's nothing scary about evil ghosts or crazy droids when you can down them with two hits.

Let NPCs die in a fountain of blood when PCs aren't looking and when they turn to face whatever just ripped Jimmy to shreds, everything's quiet and noone's there.

If you include an astromech like RLogue suggested, maybe have the ships log say they sold precisely that droid at their last stop, so why the heck is he back on board?

I like the bit with the droid. Reminds me a bit of the ending of Ghostship.

Let NPCs die in a fountain of blood when PCs aren't looking and when they turn to face whatever just ripped Jimmy to shreds, everything's quiet and noone's there.

Every time they die, it’s when the PCs have their back turned, and all they hear is “SQUISH”, and all they see when they turn around is another NPC falling to the ground who has been squished like a grape. And that’s when they feel the blood running down their backs.

So, what happens to the PCs when they run out of NPCs to have squished?

An astromech droid leaking blood from it's inner workings.

It's not bleeding itself (It has no parts that can bleed) and when the pc's open the droid they find no source from where the blood came. If you want to you can even have it spray blood like something out of EVIL DEAD...

Just the image of bleeding droid should creep the players out.

So, what happens to the PCs when they run out of NPCs to have squished?

By then they hopefully found the source. If not, they better run.

Also, to spice things up, you could let one of their NPCs - like the dude they just talked to 2 minutes ago - float outside one of the windows.

The navcom could have recorded a jump a little too close to a black hole or a sun.

Or it's a very old ship that they first have to pull out of the orbit of a black hole or a gas giant.