Jose wrote:
is there a way to avoid showing them in Workbench as they'll be using a filesystem not accessible by AmigaOS and therefore not usable ?
To just hide the icons you can use the Workbench prefs programme in 3.9, there you can choose to hide certain devices from view. They will, however still show in device listings such as file requesters and the DOS info command. To avoid this, use HDToolbox (the appropriate version for large discs!) and uncheck the automount option for whatever partitions aren't AmigaDOS. The other OS will use its own mounting routines to recognise the partition.