So what latency is acceptable in a stylus system? I don't know that either, but I'd suspect it's somewhere in the low tens of milliseconds. If they're sensing position 240 times a second, that's a little more than 4ms per sample, and that sets a floor on the responsiveness. I'd expect them to average a few samples to make a smooth experience. But if the lag is really closer to 60ms, that implies the graphics subsystem is doing some seriously heavy lifting between sensing stylus position and expressing the mark on the screen.
However, I'll point out that in iOS 9, touches are coalesced so that you can get better resolution, and predictions are available to reduce latency.
(Text summary from WWDC on this topic)
The end result is that you have one thing that actually raises latency a bit, but another that is meant to let you bring the perceived latency down. But the high sample rate is key for not getting "kinked curves" that need to be smoothed out in software.
So while the sample rate is higher than 60Hz, iOS won't deliver touches to the app any faster than 60Hz (never has). Or about 33ms between updates to apps. And then you have latency on drawing/etc on top of that. However, there is also touch prediction available which is supposed to help you get latency down by telling where the next touches
should be. But using these touches is totally up to the app developer, so it is possible that different apps will lag more than others with this setup.
That said, I'm a bit surprised that Apple's own app doesn't seem to be using the predicted touches at all. But 24-30fps video is going to introduce some issues actually measuring the real lag involved. I suspect that in this case, the 60ms is a bit high. 45ms lag actually sounds pretty close to what I'd expect from an app that's not using the predicted touches.
EDIT: After reading the whole summary, iOS 9's tweaks should help get apps to 1.5 frames of latency, which is still bigger than 33ms, but less than 66ms. So that's the "expected" range, if we use the WWDC talk as a guide... so higher than I was mathing out.