I actually ran something similar to this recently, though mine was a malevolent AI with a bad case of "A God Am I" on a space station instead of a cosmic horror on a derelict ship. Some thoughts from my experience (some of which are mentioned before as well):

1) Finding logs and "human" elements from the ship's former occupants can make it feel like the place was lived in beforehand. This is important because if your players don't have a sense of normalcy initially, it's much harder to erode it over the course of the adventure.

2) Making the ship feel alive, despite all evidence to the contrary, can evoke eldritch horror. Make it seem like the players are being watched over time, such as having the elements that Lord Torath suggests. This is especially effective if you can keep a straight face and tell the players that the doors are really not powered, that the ship is for sure shut down. I don't normally advocate for gaslighting, but in the terms of your players' characters' perceptions, this is an appropriate time to break that out. "Maybe you did leave that door open after all? Oh, you blocked it off? Huh, strange. Well it's open now, at any rate." Depending on your players, they'll likely make themselves paranoid.

3) If you're aiming for the sort of eldritch horror which revolves around an uncaring intelligence so far above comprehension as to be unknowable, it is best to keep yourself from explaining too much. If something happens and it doesn't follow the rules of the universe, ensure that your players understand that whatever happened is outside the realm of possibility... but also that it still happened.

4) Give them some amount of space to prepare for whatever happens. If you take away the safety of every single action they take, they will become demotivated and stop being invested in staying safe. Instead, let them become used to certain precautions before providing an out-of-context problem that forces them to come up with new solutions. A good example would be if the players start holing up in the hangar with their shuttle (or something like that), have that work a few times. After they have gotten used to it, rip the hangar doors off and depressurize the hangar. As they are trying to fix that, establish that their safe refuge is no longer as safe as they thought it was. (Maybe introduce monsters that come in from outside or something.)