You can create thumbnail images of whatever size you like in JuiceboxBuilder-Pro by clicking the 'Change Sizes...' button in the 'Image Size' control panel on the 'Images' tab and entering thumb width and thumb height dimensions.
JuiceboxBuilder-Pro will create thumbnails at the specified dimensions and will set the thumbWidth and thumbHeight configuration options (in the gallery's XML file) to the values that you use.
You can then edit the gallery's 'config.xml' file in a plain text editor and change the thumbWidth and thumbHeight values to whatever you like (for example, to half the actual thumbnail dimensions).
Please note that, currently, thumbnail images will be dynamically scaled to the thumbWidth and thumbHeight values only if the actual thumbnail dimensions and the thumbWidth x thumbHeight dimensions are both square.
Hopefully, in a future version of Juicebox, rectangular images will also be scaled to fill the thumbWidth x thumbHeight dimensions but this is not currently possible.