The ultimate philosophical problem that is thought over every day, “Where has the money gone?”

that is 没错。这不是一个完整的句子，实际情况是，“Where has the money gone?” 这个问句是problem 的同位语。

而that is thought over every day 是problem 的定语从句，that 是关系代词。

如果补充完整的话，可以在同位语之间加is：

The ultimate philosophical problem that isthought over every day is, “Where has the money gone?”