Does deleting folders like ".android_secure" on SD card cause interruption while turning on the phone? or Can I delete all the folders on it.

No, probably it won't interrupt the booting process --meaning your device will boot fine even if you delete all the folders in sd-card or format your sdcard. However, some of your apps will not work since '.android_secure', Android, data and few other folders (especially those whose name starts with a period(.) sign are created by system (Android OS) and thus are important folders. '.android_secure' folder holds apps that have inbuilt a2sd support and they are installed in sd-card by default even if you don't have any custom a2sd script. Similarly, other folders mentioned holds data/cache along with some parts of applications. So, removing them means making some of the apps disappear from your App Drawer or from functioning them properly. This may require you to re-install all those apps to make them working again.

So, in conclusion it is better not to delete all the folders in your sdcard. But, in case you need to make sure you keep the ones mentioned above and other system folders and remove remaining ones. That would prevent you from having any type of trouble with your device.