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When you kill an MVP, there are two types of drops: NORMAL drops (those drop on the floor, such as card drops), and MVP drops (those that directly go into your inventory). Card drops are obviously normal drops, so they're affected by the drop rate modifier, so it is indeed 0.03%.
I really don't see what's so hard to understand about this. Stop assuming there's a hidden nerf just because you haven't seen an item drop after killing 5 monsters.