Wow, I surely missed a lot
Will try to address some of the questions.
1 - AquaMail (henceforth referred to as "the app"...
) never deletes messages from mail servers, either using IMAP or POP3, when checking mail. There is simply no code there to do that.
2 - The app retrieves / updates a limited number of most recent messages during each mail check. This is the "Messages per page" setting. The mechanism of course varies between IMAP and POP3.
3 - The app keeps a limited number of recent messages in its store. This is the "Messages to keep" setting. The excess is trimmed from the app's data storage automatically, about once every 24 hours.
4 - The above sometimes causes issues with people "hiding" a lot of messages in a folder -- then after the app cleans out old stuff and checks mail, sometimes those messages are treated as new. Not good, but the alternative, keeping an eternal, untrimmed history of all hidden / deleted messages seems worse to me (we're talking about very limited devices).
5 - There is no offline access to messages past the current page for IMAP -- the app only shows what it knows is up to date. I'd like to remove this limitation, allowing offline access to the message cache past the ones known to be up to date (as there are practical reasons to want to do that).
6 - With regards to security, I feel there is nothing different about IMAP vs. POP3. Both protocols use plain text authentication (even if it's wrapped in a fancy format, like SASL PLAIN), and then SSL on top is possible for both. For SMTP, the app supports CRAM-MD5, and it works most of the time, but for POP3, there is no support for APOP or MD5 since in practice, there are too many servers where this is misconfigured, causing login errors.
7 - I wouldn't trust my own mail app to keep my personal mail archive (if it had any value). This sounds like a bad thing coming from the developer, but:
* I regularly see the app's database get corrupted, about 1-2 users per 100,000, per app upgrade. Very infrequent, but still. All of this seem to happen on Android 4.0+. Not sure if it's a SQLite bug (I know it's the best unit tested piece of software in the world, but I've seen a message where its developer admits to a data-corrupting bug, specifically in the context of Android), or an issue with ext4 specifically on Android, but...
( FWIW, I've seen K-9 lose all its data, and I've seen reports on the web about SQLite databases getting corrupted in other apps on other platforms )
* Desktop mail apps just seem (to me) to have better UIs -- hey, a 10" tablet is "large", a 10" notebook is "small". My monitors are 24"
* The ability to make backups -- you can easily copy a Thunderbird profile folder, or a Windows Live Mail message directory... Try doing that on Android (without root, I mean).
8 - POP3 support will continue, it's already there, there is absolutely no reason to take it out
9 - Boredom and stuff -- so far, it's the opposite, there is so much more work to do before the app looks and works half decent...
10 - IMAP storage -- well, Google certainly wants your whole mail archive... I've seen other services where I have accounts also offer more and more storage over the last few years. Not familiar with Daemon at all.