Shwan,
I have noticed that when you have a long URL structure with multiple folders, Google tends to lose "interest" in your deep pages.
Let me give you an example: If you have a domain called www.website.com and you have a category called gemstones. In gemstones, you have diamond as a subcategory and a solitaire as a page.
If you consider your homepage to have an importance of 1, you would not have a category page which also has an importance of greater than or equal to 1. So, your category page gets a page weight value...lets say 0.9. Now, your subcategory page is treated that same way and you give it a page weight of say 0.8. Now, your solitaire page gets a value less than 0.8. Now, if you cut out one or more levels in your URL, you have a better chance of assigning of a higher value to your page.
Now, coming to your question. Breadcrumbs are essentially meant to help your users navigate better. So, your website hiearchy (the folders, sub folders or categories, sub categories) should reflect in your breadcrumb.
So, keep your URLs short, but keep your breadcrumbs like your website flow.