Solved! Maybe not even the easiest way, but it worked for me. Humit, thanks for your tip, although I couldn't find a way to get a terminal running on my zaurus itself, it got me thinking and ended up with the following work-a-round.
Problem
Can't pass the 'new storage media detected' screen when booting into Opie using alt boot on a tosa (oz 3.5.4), probably also other models.
Fix
1. take your zaurus from the cradle and (re)boot it, choose to boot from SD/CF card in the alt boot menu
2. when the 'press any key within 5 seconds to cancel starting Opie' comes up do so (find the any key first ) and log into the console
3. before putting your zaurus back in the cradle (and lose the abbility to use the keyboard on a tosa) type '/etc/init.d/./opie start' (without the ' ', note the ./) in the console, don't press enter or OK, and put your zaurus in the cradle
>> make sure you've got a way to ssh into your zaurus, I at this point I had to put a static address for the usbd0 device in my /etc/network/interfaces
If you can't control your zaurus from another machine yet make sure you'll get this fixed first before continuing...
4. start a ssh connection from the other machine to your zaurus and log in
5. on your docked zaurus press the OK button which invokes the earlier typed '/etc/init.d/./opie start' command and loads Opie
>> on your zaurus now the 'new storage media detected screen appears
6. in the active ssh session type 'ps aux' at the console prompt and look for the process called '/opt/QtPalmtop/bin/qpe -terminal 2' and remember the process number (first nr. on the same line)
7. kill the process, in my case it was 2544 by typing 'kill 2544' at the console prompt (ssh)
>> the 'new storage media detected' screen should disappear on your zaurus and you can continue!
Gag.