1st.. the date/time on messages is in a 24 hour clock, not really a biggy but would be nice to be able to set it to a normal 12 hour clock display
There are no settings for this. It's based on your system settings. Sounds like there's something set to 24H format in your OS's time/locale settings. It does use 12H format for me.
2nd .. I have the setting set so it's supposed to mark "message read" after 1 second.. sometimes it works, some times it doesn't.. more often it doesn't.. that is really annoying.
Note that you need to have the preview pane active or open the message in another tab for that to work. For example, if you're using the arrow key to move down items in the message list really fast, a message might not be open for a full second. There's no instantly option for that. (You might be able to change the milliseconds in operaprefs.ini while Opera is closed to get under 1000, but the UI will probably reset that on you whenever you mess with the setting or similar settings.
However, Opera is intended to be used with the manual mark as read option. Opera is different in that there's an "All Messages/Unread" view and it has three different read states instead of 2. When a new message comes in, its item text in the list is bold blue to show that the message is unread and unseen. If you open/preview the message, the text will be bold black to show that the message is unread but seen. Then, after you truly read the message (only you can know that), you mark it as read with k.
It's different, but the intended way.
3rd .. the "delete permanently " is AWESOME!! but be nice if was easier to get to or have it the default setting?
Shift + DEL will invoke it. It's really convenient.
Note though that Opera Mail isn't being worked on any more.