A lot of it is flat, but they use simple bevels for buttons and other clickable elements, and its reuse on, for example, the buttons in the file manager window, looks tacky because it appears cluttered and overused. Also, excessive lines (e.g. for the window borders), high contrast colors, and small color pallet makes the overall appearance not nice to look at. Also the icon set suuuuucked.
'3D' UI elements were introduced later in AmigaOS2.0, and I remember how the user interface style guide made a big fuzz about how UI elements that appear raised are supposed to be clickable while flat or recessed elements shall be used for non-interactive or disabled UI elements which cannot be interacted with.
Actually this site is a pretty awesome collection of operating system UIs. BeOS still looks nice, almost like retro-modern pixel-art.
Older UIs like the Amiga OS one suffered from an even more limited pallet, and even worse typography.
I used BeOS as my main OS for a while and really liked it - it was very snappy and felt more "homey" (that is, more like classic MacOS) than early OSX versions did. (The browser, NetPositive, was absolutely awful though).
A lot of it is flat, but they use simple bevels for buttons and other clickable elements, and its reuse on, for example, the buttons in the file manager window, looks tacky because it appears cluttered and overused. Also, excessive lines (e.g. for the window borders), high contrast colors, and small color pallet makes the overall appearance not nice to look at. Also the icon set suuuuucked.