Your phone will accumulate all sorts of junk in time either from apps, downloads, firmware updates or any number of other sources.
So its better to reset your device when your device starts to have problems like the problems your having now with s pen etc.
Hope this helps.The Samsung Galaxy Note 3 may have been superceded by the excellent Galaxy Note 4, but last year’s top phablet is now cheaper than ever, making it a great value alternative if you don’t want to shell out for its newer, shinier cousin. At time of writing, SIM-free handsets now cost around £350, with contracts starting from around £35 a month with nothing to pay upfront for unlimited calls and texts and 4GB of 4G data. This is cheaper than the currently £469 SIM-free Note 4, although the gap has narrowed considerably between the two. If you you can push your budget slightly further, the Note 4 is no longer completely out of reach.