I kind of doubt they'd remove it from the Japanese version; as far as I know, the only censorship stuff that Japan got huffy about was the "sex"-simulators.
Nope. Especially following the Akihabara incident two years ago, violence and gore related censorship has gotten a lot stiffer in recent years. Sega and Platinum Games' MadWorld wasn't even allowed to be released in Japan without a CERO rating of Z (the equivalent of "Adults Only").
And even in cases where blood existed in some series before hand (say, fighting games like Samurai Spirits/Shodown and Guilty Gear), the blood was taken out in future releases in Japan.
So, for a shounen level franchise like Rockman, I think it goes without saying that the "blood" will likely be taken out, or recolored. Or else, Capcom will have to settle for a higher rating because the Japanese censors just won't go for anything less than a "CERO B".
That's what it looks like for Japan. Assuming this game does come over here, that's up to CoA to decide how they localize it.