Just because Bomberman has more Nintendo affiliation (and even then it isn't the deal breaker, considering Snake), it doesn't necessarily mean his inclusion would be inevitable and Simon Belmont would be not be. Belmont also has important Nintendo affiliation, especially within the NES/SNES era, as attested to by the celebrated titles ranging storied Castlevanias I-IV, some renowned among the greatest games of their systems. His iconic stature, among Konami legends, rivals that of Bomberman's as well. I would argue both characters are of equal worth, when balancing them with the weight of their valuable contributions, universal appeal, and potentially skillful move-sets. It would only be a matter of Sakurai making the final choice, if such a rare occurrence were to happen.
Ultimately, if Snake is, for whatever reason, unable to return, and Konami is willing to provide a character, then Bomberman and Simon Belmont would also ultimately be the only two reasonable alternatives. So then, the comparison is appropriate.
It's not necessarily your choice in characters that bothered me, but the lack of respect in saying so (Sakurai, "utterly stupid", "incredibly obvious").
As you have stated.