I would want to argue that such Gothic conventions as you have highlighted greatly enhance the feeling of terror that the reader experiences through reading this excellent ghost story. Clearly, the way that Miles and Flora are presented as innocents who have been corrupted by the evil Miss Jessel and Peter Quint, though the nature of that corruption is left undisclosed, greatly enhances the shocking nature of the story, whilst the appearances of the ghosts and the reactions they evoke in the narrator cause us in turn to become terrified. Note the way in which the narrator responds the second time she sees the ghost of Peter Quint in Chapter Four. The suddenness of his appearance, and the picture of him standing on the other side of the window and peering in, is terrible enough, but this is not all:
Something, however, happened this time that had not happened before; his stare into my face, through the glass and across the room was as deep and hard as then, but it quitted me for a moment during which I could still watch it, see it fix successively several other things. On the spot there came ot me the added shock of a certitude that it was not for me he had come there. He had come for someone else.
The terrifying appearance of this phantom is thus clearly linked to the way that he has come for a purpose, and that purpose is obviously related to the children and his possession of them or the malign influence that he has upon them. Connecting such a terrifying figure to such innocent "angels" and the horror experienced by the narrator causes us, in turn, to experience the same horror.