There is very useful option in Kontact clicking on a phone number or SMS in a contact to invoke the desire phone application and simply push the dial button to establish a call.
I have tried with different application as the linphone, jitsi and sflphone as external applications and got the same problem with all of them. Clicking on the phone number invoked the program and the last appeared but the phone number should be entered manually or with copy/paste nevertheless there are two options in the command line of Kontact "%n" and "%N" for entering directly the clicked number into the phone program's entry.
What should I write in the command line of Kontact to enabling direct passing of the phone number to the application with the click in order to skip necessity of entering the phone number manually ?
And the second question is if in the person contacts has the option to keep different contacts with the person as skype, googletalk and phone why there is not option in Kontact to be managed with appropriate programs ? There is option for only one application

Just check the external program's help.

For example co to a commandline and type in

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linphone --help

There you will see the line

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-c, --call               address to call right now

So to make linphone call the clicked address in Kontact, you have to type in into the settings dialog:

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linphone -c %n

and you should be fine.

If I understand your second question correctly, then you wanted to know, why skype is the only "supported" program for the telephone-numbers-actions.
The answer is quite simple: Because nobody created handlers forother applications