你的问题包含了两个问题.
1.Why 能不能引导主语从句.答案是肯定的.
例句：
Why he did this was a mystery to him until he tried working with affirmations and blurts.
选自Julia Cameron 《The Artist's Way》2002.
2.有没有“Why+从句+is because+从句”这样的结构.答案是几乎没有,至少在地道的英文里没有.这已经几乎属于洋泾浜英文了.拿你举的例子来说,
Why he was late yesterday was because the traffic was heavy.（注意主句和从句的时态要一致）
表达不好的人才会这么说.其实简单地说
He was late yesterday because the traffic was heavy.
更清晰也更符合英语习惯.