Well... Mark didn't specify which ''Hombu Dojo"... as there are a number of them in Japan, but my comments will refer to the Aikikai Hombu Dojo.
I'm not sure about the history, but having trained there, I believe the different instructors represent different "lineages" in the Aikikai.
For example, Yasuno Sensei and Endo Sensei represent the Yamaguchi Sensei line. Masuda Sensei (the head instructor) was a direct student of O-Sensei, and he represents another lineage. Arikawa Sensei (before he passed away) was also a direct student of O-Sensei and represented another lineage. I think Osawa Hayato Sensei was influenced by his late father (the previous dojo cho) Osawa Kisaburo Sensei. Irie Sensei is a student of Tada Sensei.. and so on.. Thus, the Shihans teaching at Hombu Dojo collectively help to maintain some of the main styles in the Aikikai.
This is very different from other dojo organizations which are managed by one Sensei and where the other instructors propagate the particular Sensei's style.
Having said this, I am still curious about the lineages of the following Sensei:
1) Seki Shoji Sensei
2) Yokota Yoshiaki Sensei
3) Miyamoto Tsuruzo Sensei
4) Toriumi Koichi Sensei
5) Sugawara Shigeru Sensei
6) Kanazawa Takeshi Sensei
7) Kobayashi Yukimitsu Sensei
Would be grateful if somebody could enlighten me on this