The hitbox of the hopper is in the shape of a cube, making it impossible to reach blocks underneath from above. This issue was fixed for stairs once, and I imagine the solution to the problem could be fixed in a similar way.
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Duplicate of MC-6435, please use the search function to see if your bug has already been submitted. Currently over 51% of tickets are being closed as duplicate.
@Tails I am sorry about that. I did search, but I thought that issue report was only about the collision box that you can't shoot through, and not the graphical box you see when pointing at something.