Repairing file permission is not that big of a deal. Incorrect permission can lead to application errors in extreme cases, but in general it's not going to slow down your computer. It's a myth. It's not something you have to do every morning. Once in a while, after major installation of software or OS upgrade, or after improper shutdown of the computer would be sufficient.
The reason disk utility find more erraneous permission is probably caused at the reboot when the applications shutdown they probably didn't clean up data files correctly. If you see repeated fix of files in the same directory, or if the same file keeps get corrupted, you might want to uninstall or reinstall the application that uses the corrupted file. Maybe the application is buggy. Maybe the application has not been installed correctly.
In any case, as long as the files with wrong permission are not system files, it doesn't really harm the system. Don't be too obsessed with permission repairs. Relax, and enjoy your computer more.
Daily/Weekly/Monthly cronjob is another issue. If you don't run the cron jobs, you WILL see slowdown in your system. You should run the cron jobs through Onyx or MacJanitor on a regular basis.