Is it possible to change Safari settings in a native app like following :
Nop. You can change the cookie settings for your app only.
I guess you are talking about a webview in your own application?
1) NO
You can delete them though: How to delete all cookies of UIWebView?
Also right after creation: Cookies in UIWebView
2) NO, its a system setting: UIWebView: Can You Disable Javascript?
3) There is no saved history in a webview. For cookies see 1),
for the Cache see: How to clear UIWebView cache?
Also interesting: UIWebView cache in iOS and Clearing UIWebview cache,