1. The problem is your previous AV didn't detect malware in the email folders, avast shouldn't delete the folder it will alert you to the infection and you decide how to take action.
The problem being email folders are nothing more than a single database file (so eudora is no different in this regard) and extraction of an infected email in this could corrupt the mailbox. Because of this some people recommend excluding the mailbox files from on-demand scans (program settings, exclusions, add)
2. These automated options are only available in the Pro version. This is a limitation of the Home (free) version that it has interactive input requirement, there have to be differences in the Home/Pro version and this is one of them, the programmers have to eat
In the Home version you can check the option "Don't show this window again" when the first virus warning appears, select the "No action" button. This way, no action will be taken and you will given the results at the end of the scan (and you can perform actions from there).
Over time this will become less of an issue, as the resident, on-access scanners are designed to intercept infection before it gets into your system. - There was one suggestion to place something like the eicar virus test file at the start of the first drive to be scanned in a file like ~a-eicar.com that should soon be detected and you can do the option "Don't show this window again" when the first virus warning appears, select the "No action" button. So you should have a list of files waiting your action.
3. You would effectively have to manually find the infected email, delete it, empty the deleted emails folder and compact the folders.
4. UI - You can use the skinless option (Program Settings, Common, see image) or choose a different Skin (right click the skin, Select Skin, Get more), the default one the car radio does take a little getting used to.
Version 5.0 when released will have a new GUI as there will no longer any skins, don't ask I don't know (my mind reading act) the release date.