Here’s my opinion:
Marking an empty case as pupa (or a dead, dried out insect in winter as adult) will have an effect on the phenology graph, though as @kiwifergus pointed out, the effect should be negligible in most cases.
The advantage: If I am interested in how a pupa of one species looks like, I can find it with the identify tool. And an empty case still might contain valuable ID characters.
To mark an empty pupal case as ‘Adult’ is for me the worst option, then better leave it w/o annotation.