I don't really see how that in particular is a weakness in the writing. It shows that Luke has become a very perceptive, powerful Jedi. The Emperor is arrogant enough to think his apprentice won't turn against him, which of course turns out to not be true.

I see it as far more silly that there'd be a shaft there which clearly has no purpose (it certainly wouldn't be there for aesthetic reasons if it were covered with floor plates)

Can't see it as being for venting anything either. Why would the emperor choose to have it vent under his own chamber floor?

The only reason I can see for the shaft to be there is for the Emperor's own arrogant observations. Those on the dark side clearly value power above all else. Having a view into the reactor from his own chamber is exactly the kind of thing he'd do in my opinion.