If the disk is Amiga formatted, it won't get auto-mounted, as Windows won't recognise the partition table and your Linux doesn't necessarily have a suitable filesystem available. Linux understands RDB partition tables and FFS filesystems, Ubuntu may include them as precompiled modules.
If it shows up in your device manager or /proc/partitions, then it's detected and you can attach it to WinUAE and read it inside the emulation or make an image of it with dd in Linux..
