Please understand that there is no "sedevacantist position" on anything. The word "sedevacantist" means one and only one thing.
If you believe that the present claimant to the papcy, Benedict 16,
is the pope of the Holy Catholic Church, then you
are not a sedevacantist.
On the other hand, if you believe that the present claimant to the papcy, Benedict 16,
is not the pope of the Holy Catholic Church, then you
are a sedevacantist.
"Sedevacantism" does not extend to any doctrine, liturgical rite or practice, Marian apparition, or any other thing. It is not a "movement", or a group, or a church. It is merely the recognition that the man commonly held to be the pope is, in fact, a non-Catholic, an imposter, a usurper. Period. For a more detailed and authoritative explanation of sedevacantism, I would recommend browsing The Aquinas Site at
http://sedevacantist.com/On the issue of Marian apparitions, individual sedevacantists may have differing views. I believe Our Lady of Lourdes, Our Lady of Fatima, and Our Lady of Guadelupe are true apparations of the Blessed Virgin. I believe Our Lady of Medjugorje is demonstrably a false apparition.
And though I've heard of Our Lady of Akita, I honestly have never read anything truly authoritative on what it was other than short comments here and there from people on forums such as this one. The bottom line is that if the apparition gave approval of Vatican II as you suggest, then it also is demonstrably false.
The bottom line is that there is no conflict between sedevacantism and true Marian apparitions.