It is usually recommended to restore and set up as a new phone prior to jailbreaking, too many apps on the phone tend to cause issues. But all the apps you have downloaded and purchesed through the app store will sync back to your phone after you jailbreak.
Lmao, iPhone modifications does not include pirating software. You only cheat Apple out of 30% if you pirate the software, the developers lose the other 70%. if you like the software support the developer that put their hard work into it.