what will happen to built in apps in galaxy note 1 n7000 after hard reset such as s pen?
The types of problems you're describing are generally best solved by, indeed, factory resetting. If you can't find another solution, it's pretty much always the last resort. So if you're willing to do it, it's all but guaranteed to fix the problem, unless the problem is being caused by a hardware issue.

Built-in apps will all remain. Anything that shipped with the phone will still be there. Some may have updates that need to be reapplied, but you won't lose anything that was there when you first turned on your phone after buying it.