这句话that引导的确实是pretending的宾语从句,说明了假装的具体内容,it was no use+doing+sth.这是一个比较常见的结构,至于你说的主语从句情况,其实是这样,pretending that i had not seen him是主语,改过来就是pretending that i had not seen him is no use.
假如你把 that i had not seen him当做主语,那pretending这个孤立的及物动词就无法存在下去了,因为没有宾语了,