If you used the stock file manager to search for the file, you couldn't even find it because the stock file manager doesn't show the real root fs. You have to use the terminal or a SSH/SFTP connection to your N900, so you have access to the real root fs.
If you are really sure that the config file doesn't exist, I would recommend to try uninstalling and reinstalling the kismet package through the program manager.
But remember if you can run the kismet server and it doesn't complain about a missing kismet.conf, then it does exist and you only couldn't find it.