I see both of these as trying to pose a hypothetical question, so I'd say What if there were no heaven? I believe the speaker is thinking 'Yes, there is a heaven, but what if there were not?'
Yes; though in other contexts, you might distinguish between the two forms as follows:
1. What if there were no light?
2. What if there was no light?
In #1, we pose a general question, as in your "heaven" example: "What if there were no light? How would plants grow? How would we know there were other galaxies? How could Australia ever win back the Ashes?"
There are some cases where it's grammatically incorrect to say "what if + subjunctive", as in my example #2.
In cases of "what if..." that follow the pattern of my example #1, it's probably better in formal writing to use the subjunctive, as then you will never be incorrect.
But in BrE, you'll find "what if" without the subjunctive in both formal and informa