This is really odd. There were only three titles changed (according to wiimpersonator), the manual (doesn't affect jack), the system menu (shouldn't be running once homebrew starts), and IOS59 (which like no homebrew uses).I've uploaded a video for people who haven't or aren't updating because of this. Here's what it looks like: snip
On the topic of using the Wii U pad with vWii, we clearly have some sort of channel now. It seems likely that this capacity was added to IOS59, which is interesting for two reasons: 1) this IOS was historically only used for Dragon Quest X (and could only be found on that disk), and 2) it is the only IOS with a WFS module (the custom file system used for Dragon Quest X). This makes me think that the communication with the Wii U pad may be related to WFS and/or the Wii U may use WFS for it's filesystem in general. Of course, this doesn't totally make sense I not every title will use IOS59, so it is possible that the functionality was added at a higher level like some sort of Wii U hypervisor that is running all the time, but I didn't think that was how vWii worked (I thought it talked to the graphics hardware directly).
Also worth noting, IOS59 only has one unique component (which I believe is only responsible for the WFS stuff), and since no other IOS versions changed, it is likely that is the only component with any updates. Dumping this module and looking at it (especially how the new version differs from the one on the Dragon Quest X disc) would be interesting.