1. as it is 是习语，相当于汉语的：“实际上”，“已经”等含义。请看词典释义：

2. as indeed he hadn’t 你的理解是对的。suggest 这里是“暗示”的意思。这句话的大致意思是：她暗示：他对她一直不忠诚，过去也的确一直就这样。

3. as it does  我认为是一种表示强调的用法。coming as it does after such a promising start相当于coming as it does (come) after such a promising start. 

我提供几个外刊例句，供网友体会：

1. And, maybe because it sounds so utterly impractical, especially coming, as it does, from a prison cell, the missionary preacher repeats himself to get his point across.

2. Coming as it does at the culmination of a suspiciously spirited diatribe, it unintentionally reveals what it actually is...

3. It is a remarkable document, going as it does directly to the problem of the imaginative response to art. 

4. The scale would appear as it does in Figure 7.2, where the temperature reading is either 70°F or 80°F.