To be sure it's Akarin issue I tested normal minecraft with/without forge and newest 1.12.2 Paper version, and hoppers correctly interacts with minecarts.
If you place hopper, on hopper you place rails and on rails you place minecart (with chest or hopper, same effect) hopper under rails cannot pull items from minecart.
But what about minecarts and chests/hoppers/etc.? If you place rails, one block over rails chest and on rails minecart with hopper, minecart correctly pull items from chest. That's why I think it's hopper issue, not minecarts/entities issue.
Edit. I doesn't tested if this bug exist in other versions of Minecraft, so it's maybe not only 1.12.2 issue.
To be sure it's Akarin issue I tested normal minecraft with/without forge and newest 1.12.2 Paper version, and hoppers correctly interacts with minecarts. If you place hopper, on hopper you place rails and on rails you place minecart (with chest or hopper, same effect) hopper under rails cannot pull items from minecart. But what about minecarts and chests/hoppers/etc.? If you place rails, one block over rails chest and on rails minecart with hopper, minecart correctly pull items from chest. That's why I think it's hopper issue, not minecarts/entities issue.
Edit. I doesn't tested if this bug exist in other versions of Minecraft, so it's maybe not only 1.12.2 issue.