But does the Adnoit stylus scratch the screen over prolonged use?
With proper use and care, no. There is nothing inherent in the Adonit Jot design that would cause it to have a higher probability of scratching a screen than the rubber or foam capacitive styli.
The iPad uses gorilla glass (or the equivalent), so does the Surface. Very durable. The plastic disk at the tip of the Adonit Jot is not hard enough to scratch the screen. If the plastic is cracked and the metal nub exposed, then it is possible. But that is caused by a DEFECTIVE Adonit Jot.
What typically happens, and it can happen with any stylus, is that a speck of grit attaches itself to the screen and is pushed across the screen's surface by the stylus. Depending upon the composition of that speck of grit, it is possible to scratch the screen. In terms of probability of a hardened speck scratching the screen, relatively speaking it would be most probable with the Adonit Jot (the plastic disk would keep a firm grip on the speck, followed next by a rubber tip, and lastly a foam tip stylus. Theoretically, a fingertip could cause the screen to be scratched (if that speck of grit were under the fingertip).
Common sense and good practice. Keep the screen clean. First with a clean microfiber cloth that is gently used to remove an potential grit, and then something to remove the oils... I use eye glass lens wipes. Examine your stylus before using it... even ones with the rubber or foam tips... make sure that there is no grit trapped or attached to it.
Hope this helps.