As I understand it, the difference is subtle, but it is there.
When you say something "happened", you are simply indicating that an event occurred.
When you say something "had happened", you are indicating that an event occurred at a point relative to some other point.
Using the first sentence as an example (restructuring to illustrate the point more explicitly):
Freud found out, almost by accident, how helpful his pet dog Jofi was to his patients.
It was less well known at the time that Freud had found out, almost by accident, how helpful his pet dog Jofi was to his patients.
The second sentence is a better example (while at the same time being slightly more ambiguous).
He [became] a doglover in later life when Jofi was given to him by his daughter Anna.
The sentence could be interpreted a couple of ways, but one of those ways is that being gifted with the dog Jofi is what made him a dog lover.
He had become a doglover in later life when Jofi was given to him by his daughter Anna.
This sentence implies that, at the time that he was gifted with Jofi, that he was already a dog lover, or that he had become so at an earlier point in his life than when he received the dog.
To sum up: they mean the same thing, but using "has/had" instead of just the past tense of the verb allows you to place the event in relation to another event.