But the difficulty is that by the time children reach school age,

第一个that引导的从句是表语从句，第二个that引导的从句是定语从句，修饰先行词influences．定语从句中的it是形式主语，to tell...是真正的主语 ，tell的宾语是两个whether引导的从句．
这个句子太长了呵．翻译就不必了，理清了句子结构自己翻译应该会了吧．

But the difficulty is that by the time children reach school age, there are so many other influences that it is almost impossible to tell whether girls are worse at science and maths, or whether they've been brought up to think of these subjects as
boys' territtory.
But the difficulty 作句子主语，
that引起一个表语从句，
by the time children reach school age做that表语从句的时间状语，
there are so many other influences that it is almost impossible to tell ，that表语从句中的there be 句型，句型中使用了固定用法so...that，
whether girls are worse at science and maths, or whether they've been brought up to think of these subjects as boys' terrttory. 这两个是名词从句，在这里做to tell 的宾语。
整个句子的意思是：
但是困难在于：到了孩子们上学的年级时，会有太多的影响以至于不可能说到底女孩是在数学和科学方面较弱，还是她们被抚养长大的方式让她们觉得那些科目就是男孩们的领域。

But the difficulty is that by the time children reach school