1. Is there a maximum number of files Wallpaper Slideshow Pro can handle?

Wallpaper Slideshow Pro can handle a large number of files and the only limit is 2Gb memory limit of 32bit programs. Another limit is the time needed by the program to scan the hard disk and build the files list. To give you some numbers on a fast computer Wallpaper Slideshow can easily handle 100,000 files and can be used with some delays with 1,000,000 files.

2. Does Wallpaper Slideshow has a "boss" key to quickly change current wallpaper with one selected from another folder?

Yes, Wallpaper Slideshow offers a nice solution. Wallpapers can be assigned to groups, then with a hokey it is possible to switch group and set a new wallpaper choosen from the new group.

3. Is it possible to display on primary monitor files from one folder and on the second monitor files from another folder?

Yes, it is possible by using filters. In the Filters section of the Options window select monitor #1, enable the options Include and Full File Name Contains then in the text box enter an expression to identify your folder, for example if folder name is folder1 enter: *\\folder1\\*
Do the same for monitor #2 but enter the name of the second folder: *\\folder2\\*

4. Can Wallpaper Slideshow Pro display private photos from my Flickr photostream ?

Yes, by using the Flickr plugin Wallpaper Slideshow Pro can download and display public and private photos from Flickr photostreams, groups and sets (How to use Flickr photos as Desktop Wallpapers)

5. I have a widescreen monitor and when setting my photos as wallpaper there are colored bars on both sides of my images.  Is there a way to avoid them ?

It is very easy to remove the colored bars by configuring WallpaperSS to stretch ( or crop ) your pictures. Open the WallpaperSS Pro configuration window then open the Options window Auto Resize section . Here you can choose either "Stretch and crop image to fit the screen".
Depending on the aspect ratio of your images and your monitor it is possible you need to change the value in the field "Limit for image stretching/cropping:". If the default value doesn't work (ie. images are not stretched/cropped) try raising it, here are some typical values for the Limit field:
18 : Allows to stretch/crop images with 16:10 aspect ratio
28 : Allows to stretch/crop images with 16:10 or 3:2 aspect ratio
45 : Allows to stretch/crop images with 16:10, 3:2 or 4:3 aspect ratio

6. I purchased a license of Wallpaper Slideshow Pro for my laptop. Can I install it on my desktop with the same registration key, or do I need to purchase a separate license ?

You can use the same registration on both your computers. The Wallpaper Slideshow license allows you to install the program on more than one computer provided you use the computers personally. In other words you can install and register it on all computer you wish provided ONLY ONE copy is used at any time. If the computers are used by different persons you need a license for each computer. Here is the Wallpaper Slideshow Pro License Agreement

7. I have a wide screen monitor (aspect ratio 2.38:1), most of my pictures have colored bars on both sides, is there a way to avoid them ?

You have a wide monitor with 2.38:1 aspect ratio while most pictures have 3:2 or 4:3 aspect ratio, by default WallpaperSS displays colored bars on both sides but it has an autoresize function that allows you to choose how resize pictures that doesn't fit to screen. Open the WallpaperSS settings window, click on Options the Auto Resize. In this page select the option "Stretch and Crop the image to fit the screen", choose the amount of strech/crop then click on the icon on the right of the limit value. This window allows you to easily calculate the limit used by WallpaperSS to decide whether an image may be cropped/stretched or not.

The window displays the aspect ratio of your monitor, 2.38:1 in your case, usually you don't need to move the top slider since it is already set to the aspect ratio detected by WallpaperSS. To adjust the limit value move the second slider to the aspect ratio of the pictures you wish to be cropped/stretched. All pictures with aspect ratios on the left will be cropped/stretched as well.

8. I have 3 monitors, I tried to use WallpaperSS filters to choose which pictures to display on each monitor but it seems monitor numbering of WallperSS is not the same used by "Screen Resolution" control panel window. Can this be fixed ?

Unfortunately there is no way for applications to have the same numbering used by windows, the official Microsoft answer is "It was never a design goal to provide a way for applications to label monitors with the same IDs that the screen resolution control panel uses". Starting from v4.2.3 WallpaperSS displays position and size of the selected monitor this should help to identify it.

9. On Windows 10 there is a noticeable lag/stuttering on every wallpaper change, computer stops responding and seems to be frozen for some seconds

This issue could be caused by Windows 10 choosing accent color, to disable this feature: Open Windows 10 Settings, then Personalize, in the Colors section turn off "Automatically pick an accent color from my background". Also transparency effects could cause some lag.
Outdated display adapter drivers could also cause this issue, check if there is an updated version of the drivers.