is possible to disable (maybe uninstall ) ispconfig to make some test and then re-enable (maybe reinstall ) it?
There will be problems ? I'll mess up the server?
I'am quite sure that ISPConfig is not causing the issue. ISPConfig is just a set of scripts that write the vhost config file in the sites-enabled folder, thats all. ISPConfig is not even a daemon that can caue any load when you are not changing any sttings. Also there are about 20 - 30 thousand new ispconfig installs per month which dont have such an issue, so you can assume that its not a bug in ispconfig.
You can uninstall ispconfig with the uninstall.php script which is in the install folder of the ispconfig tar.gz. But you will have to reinstall the whole Linux system when you want to install ispconfig again afterwards.
Please check the apache log files again, the global apache error.log and the error.log files in the log folders of the websites. Also check the access log files if there are any unusual requests when the problems occur. Are there any peaks in the munin graphs?