No. She's an employee (just like me). The share holders own the company.
Edit: Sorry. I think I misinterpreted what you were referring to. Yes, in the case that your spouse owns the company, they will own the company if you split. However, Japanese family law is pretty liberal when it comes to splitting assets anyway (Not entirely sure how it works for foreigners because they will get ousted from the family registry and family law will not apply to them). Basically, splitting up in Japan is tricky no matter what you do, so it is reasonable to exercise caution.
Edit: Sorry. I think I misinterpreted what you were referring to. Yes, in the case that your spouse owns the company, they will own the company if you split. However, Japanese family law is pretty liberal when it comes to splitting assets anyway (Not entirely sure how it works for foreigners because they will get ousted from the family registry and family law will not apply to them). Basically, splitting up in Japan is tricky no matter what you do, so it is reasonable to exercise caution.