But surely there won’t be physical dragons. More than the three that dany has. Could the dragons in Mel’s vision not be a metaphor for Jon snow’s real daddy.

It’s hard to say. Sometimes dragons are metaphorical – the prophecies in Dunk and Egg, for example. However, with Dany, the dragons are quite physical. 

So the stone dragon under Winterfell could well be real. It may be the case that one of Dany’s dragons doesn’t make it to the final battle either because of Victarion or the Dance with Aegon. In which case the dragon under Winterfell may be Drogon’s opposite number.