(I subsitute smart for nice as more idiomatic.)
- It wasn't a smart decision because you had already found out that your diary had been stolen.
- It wasn't a smart decision because you already found out that your diary had been stolen.
The time you are talking about—what linguists often call ‘Reference Time’ (RT)—is the time when your friend made the decision. The important thing about his discovery of the theft is that it gave rise to a state of knowledge at RT. This is the standard occasion for using a perfect: in this case, a past perfect, because you are relating the prior event to a state at RT. Version 1 is preferred:
... you had already found out ...
The issue of ‘exact time’ does not arise here, because
- No ‘exact time’ is expressed for the discovery, and that's all the grammar knows about. Grammar is like a computer program, irredeemably literal-minded: the fact that you know when it took place is irrelevant.
More importantly, the issue only arises with a present RT. The present perfect is is a present tense and cannot be used with time expressions which exclude the present RT. Those expressions require a simple past.
∗ You have found out about it yesterday.
okYou found out about it yesterday.
But with a past RT, there is no ‘past-in-past’ form which contrasts with the past perfect; the past perfect is used for both prior actions and resulting present states; so explicit references to prior times are acceptable.
okYou had found out about it the day before.
Your question about sequence with two past perfects is something that mere grammatical rules cannot resolve. Remember: English has only two ‘absolute’ tenses (past and non-past) and two ‘relative’ tenses (past perfect and present perfect) to express the entire range of possible time references. That being the case, tense is not really capable of distinguishing time references more than two deep. Most of the burden of pinning down times is handled a) by specific temporal expressions like ‘yesterday’ and ‘when I got home’, and b) by inference from the knowledge shared by speaker and hearer—context ...
Context, context, context!
... In the case at hand, inference handles everything perfectly adequately. Your friend could hardly have discovered that his diary was stolen before it was in fact stolen; ordinary knowledge of the real world allows him to understand what you mean.
∗ marks a usage as unacceptable
ok marks a usage as acceptable