It effectively says the following (but with flavor and emphasis):
No one believes he did it because he was a sensible man.
Miss Honey is talking about her father's death by suicide. Many people are uncomfortable talking about suicide (especially of family members), and it's particularly inappropriate to bring it up around children (such as Matilda), so she hesitates and speaks indirectly.
You see, no one could believe that he would ever have done it. He was such a very sane and sensible man.
At this point, the reader doesn't know what happened (i.e., what "it" refers to), but we know:
Something happened that drew attention. Furthermore, "no one could believe" implies many people are aware, so it must have been major.
The people who are aware were (in some unstated way) led to believe Miss Honey's father did it.
People consider Miss Honey's father "sane and sensible", so they don't believe he actually did it, because it contradicts their understanding of Miss Honey's father: his character and personality.
The "You see, ..." basically alerts Matilda that Miss Honey is about to explain something carefully (and maybe it's also part of her hesitation).
Saying "no one could believe" is slightly stronger than saying "no one believed", as it implies that they are incapable of believing it. Although, since "no one could believe" is such a standard thing to say, it's emphasis isn't that strong.
Adding in the "ever" again emphasizes the strength of their belief. The time period it refers to is Miss Honey's father's lifespan: according to their beliefs, at no point in his life would he have done it.
I believe "would ever have" (4,980,000 Google hits) is an alternative to "would have ever" (115,000,000 Google hits), so I don't see a difference in meaning between:
would ever have done
would have ever done
Which you say is probably more related to where you grew up (or, in this case, where Miss Honey grew up).
we use "would have done" to imagine something that did not happen
It's possible to use it for scenarios that happened too (by someone other than the subject): "I would have done the same thing" implies someone else did it, but if it were my decision, I would be willing to do it too.
With Miss Honey's father's suicide, it happened. With this scenario in mind, we have:
- "he would have done it" => "he would be willing to do it"
- "no one believes he would have done it" => "no one believes he would be willing to do it"
- "no one could believe that he would ever have done it" => "no one in able to believe he would be willing to do it (at any point in his life)"
Which is a long-winded way of saying "no one believes he did it".
so does it means that Miss honey's father could kill himself at any time, but he didn't
I don't think this description is accurate. Instead, people generally thought Miss Honey's father is "sane and sensible", and that he simply would not kill himself: it is not something he would be willing to do. The idea of Miss Honey's father killing himself is something that would not have entered their minds.
The passage is meant to provoke suspicion in the reader: if he didn't kill himself, then how did he die?