Water Hammer from Upstairs Toilet
That's not water hammer, or it's very little at best. That sounds more like the fact that your fill valve is getting a little old and is banging shut harder than it used to. I would just leave it, but if it bugs you, replace the fill valve. There are newer ones on the market now called "quiet" or even "silent" fill valves. They are a little more money, but you seem like the kind of person that would want that.

http://www.mechanicalcaveman.com/best-toilet-fill-valve-review-flush-system-kit-replacement/