Apple Pencil is more durable than you’d think. Normal jostling while it’s charging doesn’t really affect it. With regards to USB C, I think they’re trying it out on the new iPads because these are ostensibly their “pro” iOS devices, so it makes sense to put higher-throughput ports on them first.
I'm less worried about the pencil than I am the port/connector. The pencil is pretty long and there's not much slop back front to back in that port to deal with jostling.
