Plot Holes that Are Really Clues and Clue Timing

Lately I've been doing a lot of work on revisions, and I came across this one plot hole. Essentially, the insolvent estate my MC inherits shouldn't be in such dire straights.

At least, that's what my MC thinks.

In reality, when you look at the story more broadly, there are very good reasons for the estate's financial trouble.

So, what I thought was a plot hole is actually a clue that something is amiss and my MC is being lied to. This is a good thing. I'm writing a mystery; there need to be clues. This revelation got me to thinking. Sometimes it's okay if part of a plot thread doesn't make sense to the MC (or to the reader, for that matter). It's okay if the MC and her friends don't have an instant answer for everything. Because, if they're asking a question they don't have an answer for, they (and hopefully the reader) will be intrigued. Their curiosity will be piqued. And curiosity will pull a reader through the story (I read a blog post on this recently, which of course now I'm having trouble finding. Should I spot it again, I shall provide linkage.)

Now, that said, it is bad if I don't have an explanation. That is a plot hole.

The next thing I got thinking about was that now I knew that this thing was a clue and not a plot hole, would it give away who my villain is too soon? Only if I let it. I've got two options for dealing with this:
1. Let the villain lie and give a false explanation for the lack of funds that placates my MC for a short while, until she figures out the villain is lying. This explanation could also be unsatisfactory or throw suspicion on another character.
2. Put off the realization that there should be more money in the estate. She's busy, and maybe she thought she had an explanation for the lack of funds, then she realizes that no, her explanation doesn't work after all.
Bonus option: Do both. She doesn't realize there's an issue until I need her to (assuming I can pull that off without it seeming contrived) and once she does she asks about it and gets lied to.

I'm thinking I'm going to do both, then turn the story over to alpha readers and see what they think.

So, to summarize this post:

• It's okay if not everything has a nice, pretty little bow of explanation. In the middle of a story things that are all tied up and pretty can be boring. Unanswered questions things that don't make sense are more interesting.
• There are a couple ways clues can be timed to have the desired impact. 

What do you think of these ideas? Have anything to add? Tell me in a comment!