I think you could simplify this even further, and just have a morale penalty for all crew members if the ship is significantly below its optimal number of crew members.

While specialties are obviously important, on a real-life ship everybody pitches in when you are short-handed. Even if the engineer takes the brunt of it when you are short on engineers, your crew is a team, and everyone runs short of sleep when there is too much work to go round.

Given the feel of your game, I'd also go with something like that after carefully re-thinking it through. Actual crew count would be more relevant.

If its a 4 crew ships, having less OR more crew could both result in morale drops, so that, when attempting to go anywhere over 4 (and invading everybody else's personal space), you'd need to be damn sure you need that scientist onboard.

• Crew Capacity: maximum number of crew members you can hire for this ship
• Optimal Crew: A range given for each ship's optimal number of crew members. If outside the range, crew receive a morale penalty (i.e understaffed or crowded)
• Cargo Space: measured in cubic meters - how much cargo you can carry on the ship, and all non-mounted equipment, including Rations, takes up cargo space.
• Sensor Slots: how many sensors you can equip on this ship (excluding the default build in Directional Radiowave which comes standard with all)
• Advanced Equipment Slot: Used for the Scientific Scanner and for the Ram Scoop.
• Fuel Capacity: Something I overlooked. Chemical fuel is used as you free-fly around (only if you accelerate/decelerate), while Deuterium fuel would limit to how big of hops you can make between star systems

• Heat Sensors: require one free sensor slot
• Planetary Sensors: require one free sensor slot
• Scientific Sensors: require one free sensor slot - this only provides the location of spatial anomalies, not the ability to scan them (locations become an item and can be sold)
• Scientific Scanner: requires one free Advanced Equipment Slot - provides the ability to scan spatial anomalies, requires Scientist to operate
• Ram Scoop: requires one free Advanced Equipment Slot - if you fly though a Gas giant with this equipped, it replenishes your Deuterium fuel supply.

• Cook: If present on board, and you give more than 1 ration a day to your crew, gives a morale boost. Only one allowed on-board.
• Xenobiologist: If present, you can send a simple exploration mission anywhere on a habitable world that has a small chance to refill your rations.

Between two different types of fuel, and the need to balance available rations vs cargo space, there seems to be a lot of ways for a player to lose the game just by mismanaging basic resources.

Hm, perhaps. Fuel can just be simplified to one type - Deuterium, and not worry about free-flight, giving a sci-fi explanation that it uses the Fusion reactors and some insignificant (read: not having a gameplay effect) amounts of Deuterium.

As for Rations and Cargo space - rations don't have to take up huge amounts of space, the numbers can be adjusted so that for a decent sized journey of say, an in-game week, the rations necessary, even with max crew, would take up 1% of your cargo. There's a lot of factors involved, but what I mean is that rations don't have to eat up a lot of space.

I'm all for simplifying things, in fact the fuel simplification doesn't sound bad at all - but I'm also ok with making the player lose the game because of resource mismanagement (to some degree). There's no combat, no real outside threats to your ship at all, so I was initially struggling of ways to introduce difficulty.

I'm curious whether you feel it is useful to have loss conditions at all in a non-combat exploration game with no external risks?

Well, among one of the many games that inspired me is a game called Motherload, a flash based 2d grid-digger game. It was fairly popular, and there's even a greenlight version being made. The game had you digging for different minerals, then coming back to the top to sell them. It had cargo size limits, as well as limited fuel - and essentially had you die when you ran out of fuel. Despite that, it was still interesting, and kind of addictive to push yourself to go digging deeper for better materials. It's one of the feelings I was hoping to re-create (only in space).

The idea of just getting a high score as an ultimate goal doesn't have much of an appeal to me, and neither does time-limited exploration. I have some vague ideas about other possible end-game goals - possibly involving unique missions and solving some mystery - but I'm holding off on that until I get the basic gameplay settled.