Well, I personally prefer complete stories not some bit and pieces that could potentially be interesting, but never elaborate upon not because author can't do that, but because he doesn't give a damn about it.
Wait, what?
And what about some general information why it did happen? It is very important thing to the Castlevania (old) timeline and to the OOE storyline. OOE was a perfect opportunity to finally let that cat out of bag. I mean, story was directly related to the Belmonts dissappearance and it never was properly explained why it happened in the first place. They just...dissappeared and that's it. Sorry, but it is shitty storytelling in its purest, no matter how you look at it.
And idea that you don't need to know all details in the story, works only when said details are really insiginificant. Other wise you just accept that author didn't care enough to explain important plot points and treat as it's a normal thing. For that matter Belmonts disapperance is not an insignificant detail by any margin.
I think for OoE it was more of a setting thing. Building mystery with omission. The plot itself was not terribly involved with the Belmont sub-plot except for a plot by Balthier that only required the whereabouts of the Belmonts, and not why they were amnesia-stricken. Though it would be interesting to know why! But Shanoa or the player knowing wouldn't affect the story at all. Instead, it would probably give rise to a desire to see that conflict resolved, despite that not being the premise of the story. If that would happen, the story would become convoluted because it'd gain two conflicts with competing importance.
In regards to the meta-story, it's mostly vague rather than filled with a lack of logic or inconsistency. Of course, you said that. But while incomplete, it still doesn't contradict itself. So I don't really find those sort of elements detrimental to the storytelling. I'm not sure how it's really significant when it's never directly referenced in a way so that the plot, internal logic, or conflict demands it.
Now a real plot hole would be SoTN's inverted castle. because how does that even pop up, why is shaft a ghost still, i thought he was defeated, god iga you are terrible go rot in hell why dont yu asasd i