http://www.aruze.com/en/ir/release/2007/20071003_2e.pdf
This report indicates that as far as the company goes, as of 21 September this year it was renamed Azure Global Trading and is now in-charge of purchases for the parent company. It no longer has anything to do with game development.
So.... where did they go? Today many stores in Japan started selling Lost Odyssey a day early, and I managed to get a hold of the credits from the manual. Here is the complete list of ex-Nautilus staff that worked on the game as part of Feelplus:
Art Director: Takamasa Ohsawa
Program Lead: Nobuyuki Yanagisawa
Animation Lead: Takeshi Toyoda
Environment Model Lead: Junichiro Asakura
CG Cinematics Lead: Izumi Obata
Audio Lead: Hirotomi Imoto
System Program: Takaaki Ishikawa, Izumi Hamamoto
Battle Program: Masahiro Honma
World Map Program: Suguru Yokoyama
Battle Planner: Takehiro Ishida
Character Model Artists: Mieko Okuto, Kazuna Mikamoto, Hiroko Ito, Koki Nakadai, Yoshiyuki Yanagisawa
Motion Artists: Kazuya Nishimura, Hiroshi Mitsuzuka, Isao Takeuchi, Naohiro Endo
Background Map Model Artists: Ayumu Kuboya, Seiji Tokizawa, Hiroki Nakamura, Junichi Morita, Ikuo Yamazaki, Noriko Yoshida
Effect Artists: Hisaya Suzuki, Katsunori Ootsuka, Kumiko Takada
Visual Production Manager: Shinya Miyakawa
Cut Scene Visual Artists: Hideki Kubo, Masahiro Satou, Fumiyo Tanaka, Minoru Saegusa
CG Artists: Takayuki Higurashi, Hiroshi Yamamoto, Nozomi Sanada, Norio Tachikawa, Tomoaki Morizumi, Shigeru Kasai
Sound Artists: Masakatsu Tamura, Tomoko Imoto
Not all Nautilus staff made the transition to Feelplus, and there are some notable losses. The real time cutscene director Toshiyuki Terada and the creator of Shadow Hearts itself Matsuzo Machida are both missing in the transition. Various designers and planners also seem to not have made their way across. Still it is good to see over 40 members of the staff that have worked together since the first Shadow Hearts is still together. Hopefully Sakaguchi makes good use of their talent and experience to create even more ambitious RPGs in the years to come.