In Japanese, "niisan" and "nissan" sound different enough that they're unlikely to be confused.
I was really surprised when I lived in Japan that my American sensibilities about what words sounded like other words were not the same as a Japanese person's.
For example, I knew a girl named Junko (Pronounced like June ko), and when I asked my other Japanese friend if her name sounds like the Japanese word for poop, "unko", he said it never occurred to him. They're pronounced almost identically, even in Japanese, but the Japanese spelling is more like jyu-n-ko vs u-n-ko, and I think that slight "y" sound in "jyu" just makes things different somehow.