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I read, that each runlevel has its own set of services or daemons, which can be looked up in /etc/rcX.d (X for the respect runlevel), there are scripts which names start with S and start services of the runlevel, there are also scripts that starts with a K, they are killing-scripts to stop a service from running.

Now, my question points to the fact, that it is possible to enter each runlevel from each other runlevels (2-5). for instance one can enter runlevel 1 from runlevel 2,3,4 or 5. Since each of them have different sets of services, why there is only one set of killing scripts? When I compare /etc/rc1.d and /etc/rc5.d there are services in runlevel 5 for which no killing script exist in runlevel 1. What happens to theese services when transiting runlevels?

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You are thinking of this in an incorrect way; the K scripts which are present for instance in runlevel 3 are not meant to be for killing stuff before entering runlevel 3, but when exiting runlevel 3 before entering some other.

So transitioning from runlevel 5 to runlevel 1 would first execute the Kill scripts in /etc/rc5.d (which would match the Start scripts executed when entering there) then the Start scripts in /etc/rc1.d

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