Sub-zero was killed in two endings:
1.) Hotaru
2.) Noob-Smoke
But don't worry, I don't think this will mean Subby is gone for good.

i doubt either of those endings actually happened. Boon said that all future MK games will have Scorpion and Sub-Zero in them. if every ending did come true then MK's story would be very confusing.

If every ending were true, then Quan Chi would be the ruler of Netherrealm as the only one alive.

if every ending were true.
Shinnok would be defeated.
Shinnok would have won.
Hotaru would have died like 3 or 4 times
Li Mei would rule with the Dragon King
Scorpion killed the Dragon King
yea it would be a fucked up story.

I think eventually the only canon ending will be Sub-Zero's

HAve you ever played another MK game before? How many character's endings end up either with that character dying, another character dying, or that character ruling the world/saving everyone/etc?
In EVERY game something dramatic happens in one character's ending. It doesn't mean it actually happens. Rather, some things do happen from one ending, but not everything.
For example: Noob Saibot has been revealed as Sub-Zero's brother (patting myself on the back for figuring that out about 5 years ago). But Sub-Zero doesn't have to die for Noob's ending to be accurate. We now know that Noob is Sub's brother, so nothing else has to happen. Just like in MK2, Scorpion finds out that this Sub-Zero is actually the younger brother of the Sub-Zero from MK. That'd doesn't mean Scorpion won the tournament, as he ending further states, it just shows us something new about Sub and Scorp.
And also, the Dragon King dies in about 15 endings in Deception...yet im sure his scaly ass is gonna be back for MK7.
Don't assume just because one thing happens in someone's ending that it actually happens in the storyline, otherwise there would only be about one or two characters left alive for mortal kombat anymore.

I think that the only way the ending is true is if the character beats the game. Im not talking about people beating it I mean like the characters like Liu kang who won all of them until mk4 and kung lao who won mkda and even Li Mei who won the FAKE tournament. Although I might be wrong I think its possible. I think alot of the endings are what would have happened if that certain character was to win the tournament.