Is a shut down procedure needed?

It's necessary when MP and VM are used, but it's up to the OS how to shut down.

Zorro-compatibility?

Not in the beginning, if at all. Speed is critical and trying to implement zorro-compatibility will dramatically increase the cost and complexity of the main board. This only applies to the AmigaONE 4000.
This should just about be the only classic Amiga aspect, which the AmigaONE can't cover. Eyetech suggests you replace your Zorro expansions with PCI counterparts, wherever possible.
However Eyetech are looking for a reliable solution to this, if it can be done. The AmigaONE 1200 will apparently not feature this and will therefore be out first.

What about the Early Startup Menu on SVGA screens?

This will be done through third party providers and the software for that will be stored in the FlashROM residing on the AmigaONE.

NOTE: This isn't part of the official FAQ and there may be errors in it as I've only tried to interpret and summarize the information given on the AmigaONE mailinglist.