Yu-Gi-Oh!

Well you could argue that Yugi's deck in the original series wasn't heroic either. He had cards like Summoned Skull and Mammoth Graveyard that were very much evil looking monsters. And continuing into GX Edo/Aster Phoenix who despite starting out as a rival he was never really bad and helps the good guys out several times, had D-Heroes including Plasma who is literally named after blood. Given that characters like Spawn and Edward Scissorhands were early inspirations for Takahashi, "looks scary but is good deep down" pops up every as a reoccurring element in the series even if some characters very obviously wear their evil on their sleeve.

My guess is that they chose it because they wanted to keep him as an intimidating rival, whose methods/goals aren't always clear. Him having a scary-looking deck adds to that mystique.