@borut.podlipnik
You can change the shape of the thumbnails with thumbWidth and thumbHeight (via the 'Thumb Width' and 'Thumb Height' sliders in the 'Thumbnail' control panel). They do not need to be square but they will all be the same size as each other.
However, images in folder thumbs (probably created by Lightroom) are correct - not cropped!
The thumbnails exported by Lightroom are not cropped (as you have discovered). Lightroom uses the thumbWidth and thumbHeight values as maximum bounds when resizing the images and their aspect ratios are respected.
However, Juicebox will always dynamically scale the thumbnail images to fill the thumbnail dimensions (with cropping if the aspect ratios do not match) when the gallery is displayed.
Even though JuiceboxBuilder-Pro crops thumbnails to the exact thumbnail dimensions and Lightroom does not, if you view galleries (built with JuiceboxBuilder-Pro and Lightroom) with the same thumbWidth and thumbHeight values, the galleries (and thumbnails in particular) will look the same.
There is no way to change this.
The only thing you could do is create your own set of scaled-to-fit thumbnail images (in Lightroom, Photoshop or another imaging program) and replace the ones in the 'thumbs' folder.
Please bear in mind that it would still not be possible to have thumbnail images of different sizes. All thumbnail images will be displayed at the thumbWidth and thumbHeight dimensions. If you have images of varying aspect ratios, you may need to pad your thumbnail canvas with blank space (at the top and bottom or left and right) to fill the thumbnail dimensions.
If you like, you can post suggestions for future versions in the Feature Requests forum thread.
This keeps all the ideas together and ensures that they are not overlooked by the developers.
I do not know the likelihood of any suggestions being implemented but this is certainly the best place for all ideas.
Thank you.