Regarding
John's apparent/possible death
Bran's vision
...his bastard brother Jon sleeping alone in a cold bed, his skin growing pale and hard as the memory of all warmth fled from him...
May suggest
that Jon will recover, perhaps as something slightly different after his death/injury. Loss of his memory as a warm being may change him in significant ways, though.
Then, poking through Daenery's vision:
A blue flower grew from a chink in a wall of ice, and filled the air with sweetness.
May suggest
that Jon, the son of Lyanna (who loved blue roses) will bloom at the wall, and the sweetness filled air suggests that he will become personally (possibly romantically) important or valuable to Daenerys.
That same vision also has:
A corpse stood at the prow of a ship, eyes bright in his dead face, grey lips smiling sadly.
If Jon
does die and is brought to life again, (which is the only way he can be released from his covenant to the Night's Watch), this could portend his coming to Daenerys. There are a lot of reasons this could be another person, but keep in mind that Winter is coming, and chances are good the only way Westeros will survive is with the willing aid of the dragons.
And
I don't know that Daenerys will have any reason to search out Jon, but Jon will certainly have reason to go to Daenerys. However, it's quite possible that he would go seek her help even while under the covenant of the Night's Watch. He doesn't have to be released from his promise to seek her help. On the other hand he may not be able to fill the air with "sweetness" for Daenerys if he is still under covenant. On the Others other hand the book is filled with examples of people with strong convictions which they then broke for what seemed to them worthy reasons, so he may not need to die to be convinced to break his oath.
Other visions, particularly about lightbringer and that Daenerys must touch the light also suggest a meeting of some sort, but are significantly less strong in terms of romantic inclinations towards each other.