Well yeah, some things are just off-limits aren't they? My brother had trouble finding an appartment so he ended up signing up for one under his girlfriend's (now wife) name. That sort of stuff. I believe nationality is also an issue when you want to make a loan. My father (full Dutch) complained about that when he wanted to do some arbitrage on the Yen, he wasn't allowed to borrow any money!!
Again, I haven't experienced it myself so I do not know the fine details, and I think that there are some appartments rentable by foreigners, or loans for foreigners. I just have the impression that they're harder to find or that there are more restrictions when you don't have the Japanese nationality.