Finding old emails in the Finder

Hi, there,
My iMac is used for my business, so I keep (one can call it archive) many important emails in their specific folders, some emails are 4-5 years old.
I'm wondering what is the system, or logic, based on how the operating system is keeping emails in the Finder... Of course, one can retrieve old emails (that were not trashed) thru Apple’s Mail itself, but the reason for asking is, I backup some of those mailboxes, the important stuff, as part of my routine nightly backup, and in case of emergency, I may need to sort them out manually thru the Finder (am I right?)...
My questions:
1. For some odd reason I have TWO places where my Mac stores those emails: in my (User>Mail>V2> Mailboxes>specific mailbox) folder, and also in my (User>Library>Mail>V2> Mailboxes>specific mailbox) folder... Is that normal? The V2 folder in my User folder is 14 GB, while the V2 in the User>Library is 19 GB. I’m not even sure now WHICH of those 2 folders my backup software is archiving...
2. Every mailbox has a folder with a long name starting with CECD2235-.... and inside there are bunch of folder named with single digits, and inside each a “Messages” folder with the emails. But there’s no logic how the system is sorting those folders, the emails are all over the place.... I sure can’t find an email based on the date it was received...
3. One of the annoying things in the Finder is, once I open a folder the “modification date” immediately changes to THE MINUTE IT WAS OPENED, so in the future I can’t rely on sorting those folders by dates...
Some education here would be appreciated...

Thanks, Eric...
1. So should I just DELETE that MAIL folder I have in my user folder?
2. Of course, I can sort any folder items in the Finder by name, date modified, size, etc., BUT as we all know so well, the OS has not been very good in sorting the CONTENT of a folder, especially with several nested folders down, depicting the TRUE date of modification of the LATEST file inside.... So here, the latest example, I'm opening now a folder whose modification date shows Jan. 27, 2015, but inside there are files (nested in a sub-folder) with mod. date of Jan. 29...
3. Normal, but ANNOYING... I guess no way to tell my Mac to stop this behavior, right? It makes little sense...

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Finding old emails in the Finder

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