Why was Ueda Ryouhei appointed the head of the Yoshioka clan and not Seijuurou's son?
Vagabond is a fictionalized interpretation of Musashi's life adapted from Eiji Yoshikawa's Musashi. The novel is a dramatization and not really historically accurate, even though many people have started to take Yoshikawa's book as historical due to it's popularity.

Now why was there no mention of Matashichiro, the youngest of the Yoshioka brothers? It's better (commercially) to not to mention the fact that Musashi killed a 12 year old boy.