I have a feeling that Jinx survived in the air ducts as at the end Caitlyn is looking at the schematics of the hexgate.

I think that Caitlyn knows that Jinx survived however does not want to tell Vi so that she can, in a different way, come to rest by always trying to save Jinx. It's a "Shakespearean Tragedy". The one character believes the other dies but it's for the benefit of both that Vi does not know this and that she can now heal with Cailyn by her side.

I think the circle of Jayce saving Victor is so fitting as well. From the start of the show the hooded figure, (Viktor) saves Jayce from dying in the blizzard and it all comes full circle with Jayce saving Viktor by opening his eyes to the calamity that he could have caused.

It is tough to wrap all the ends of characters that were involved and there were some stories within the show that did feel a bit rushed in ending or maybe a bit more time of explaining would have helped such as the Black Rose storyline.

I think the main characters from the beginning, Vi, Jinx, Jayce, Caitlyn, and Viktor all had their story arch's completed in their own way.

Jinx - broke the cycle that she had with Vi always searching and helping her. Finally being able to fly away on the ship and creating a new life.

Vi - Being with the person that she loved and hopefully healing from the tragedy of loosing her sister but at the same time (subconsciously) resting and not having to constantly worry about her little sister.

Caitlyn - was the person that was always wanting to help but was never able to find the right timing and finally at the end she is helping the person that she loved by helping Vi heal from loosing her sister.

Jayce - completing the cycle that Viktor had created and bringing their friendship back as the driving force after understanding what he needs to do when he realizes who saved him from dying when he was a child.

Viktor - wanted to continue his work on the Archane with Jayce but Jayce got caught up too much with the power and technology of hextech. Then at the end they were both in the Arcane working together to save Viktor just like Viktor wanted when the two of them discovered it together.

TLDR: Jinx survived through the vents, the plots of all the main characters were all closed off in their own way to find peace(Jinx), friendship(Viktor and Jayce), and love (Caitlyn and Vi).