I don't think this is a plot hole, and with dnd, in Faerun, the rules and lore can sometimes get muddle. For example there are occasionally Good Aligned Demons or Devils which lore-wise should be nigh impossible. Therefor, it isn't out of the question that a Vampire Spawn could still have their soul, possibly due to the machinations of their lord, in this case Salazar. In fact it is possible Salazar currently has his soul cause that makes it easier to puppet his Thralls and the reason he doesn't destroy it is cause Astarion is his favorite plaything. With this it wouldn't be impossible that the deal Astarion could make is something along the lines of "When your soul is released from the clutches of your Master it will transfer to Raphael." This would fit the conflict of him possibly having to go from one horrid slavedriver to another.
That's not how the economy of souls work in Faerun.
There are clearly established rules for where souls go upon death, because the gods themselves depend on the worship of mortals (Ao decreed this), for which they provide them afterlives. The devils need an infinite amount of souls to combat the infinite armies of demons.
Upon death the soul leaves the body, crosses the Astral Plane and arrives at the city of judgement, where Kelemvor decides whether the soul was faithless, faithful or false, and then the soul is picked up by the proper deity and taken to it's afterlife.
We know that Astarion died, because he was murdered by a bunch of gur, and Cazador bit Astarion so he returned as undead. Astarion the person has a soul. We know this. The question is whether he has his soul joined to his body or not. I'm leaning towards yes, but the game will have to clarify that for us tbh.
But it is also possible to bring back a soul or take a soul. Additionally ghosts and revenants are creatures that can be encountered in Faerun, as in the soul does not properly pass and therefor forms these beings of regret or revenge. Additionally, as far as I am aware, the soul does not pass immediately after death but after an amount of time after death, that is why lower level clerics can still resurrect people within a short amount of time without having to drag a soul from heaven, and if I remember correctly this time is the Crux of the ritual to become a lich, which leads to my final exception being that there are many ways to trap, suck, or enthrall a soul so that it stays on the mortal plane.
Thus considering how possible it is for a soul to fail to pass to the afterlife properly, and considering the unknown powers Salazar may indeed possess, I think it is very likely that this supposedly powerful vampire lord could have stopped a soul from leaving Faerun.
Though I could be very wrong, others know the lore better than me and even though there are a ton of exceptions, that does not change that the rule exists, I think we will have to wait and see.
Edit: I forgot to respond to last part, I think his soul is connected to his body somewhat but under Salazars ownership, but I can definitely be proven wrong.
