I guess that by "Blackberry mouse" you refer to the trackpad that was present on models such as BB Torch 9860.
I think the key thing here is that, per design of these devices, the swipe gesture using the trackpad serves a different purpose: performing browser scroll at the level of the entire page. You can see such scroll active using the trackpad when the page is overflowing the screen size. Differently, the scrolling at the level of dojox/mobile/ScrollableView often concerns only part of the screen (the remaining being for instance headers and/or footers), and there can even be more than one scrollable area inside the page. Hence, it wouldn't be practical to scroll them using the trackpad, since it would first require to identify the element which should scroll - for that you'd need to click it, which may wrongly trigger a button action for instance.
Try for instance to scroll using the trackpad on this BB sample page: http://blackberry.github.io/WebWorks-Samples/kitchenSink/html/css3/overflow.html. It contains several scrollable areas, and the trackpad only allows to scroll the entire page, not the individual scrolling elements.
If in your dojox/mobile app you don't need fixed headers or footers, just use a dojox/mobile/View instead of ScrollableView. This way the content can overflow the page size, and you'll be able to scroll the entire page using the BB trackpad.
All in one, I think the behavior you observe is the expected one.