"Mortal Kombat has no presence in Japan" is a bit disingenuous. It's not being sold since the first game(and I think maybe some of 2?), due to the violent nature of the game itself. It however is on the black market often because people still want it. It has a smaller presence, and one I agree would affect Nintendo's thought on having it in Smash. Since they can't fully promote it very well at that point. I'd see a Spirit Event as possile.
However, the whole "they can't work in Smash" isn't a good point. Blood and Gore is not a requirement, and having forceful "violent" moves has been done just fine with Ridley. They can easily transfer their personality and style very well. That doesn't mean it's a logical representation, since the blood/gore is important to the series(though Nintendo has legally had it censored before, so it's clear that it can get away with it fine). Never mind Mortal Kombat VS DC Universe(the official game number 8 in the MK universe itself) shows it's most definitely not an issue to censor it. Not speaking on how good a game it is. It's "okay" at best.
I don't think they're getting in regardless, but it's not due to a lack of presence(it has the popularity worldwide to justify it), it's due to it being unable to be sold, making it a difficult series to promote and Sakurai probably not wanting to censor the point behind the series that much. Of course, we don't actually know how Sakurai nor Nintendo feel, but I doubt them. Seeing the lack of actual ability to sell, that also means a Spirit Event might be avoided for similar reasons. On another note, Nintendo has more than once had exclusive content in their MK ports before, so it's not like they don't have good ties with the series. It had more Kharacters in the Wii version of Armageddon(and the only thing it lacked was online, since MKWii had to have it first), Khameleon alone was a Nintendo exclusive, and then there's stuff like various DLC characters/options like Shao Kahn. They do clearly have a decent tie to the series, whether it's censoring or exclusive, that other console companies don't have. Means little, but at least we know they see it as something they take an interest in enough for exclusive content. It means jack for Smash, though, due to other factors.