this is an interesting topic. Putting VUE.js inside of Hype shouldn't be a problem. At least when sticking it into a container. As for managing state across the whole document I do suspect that the virtual DOM and Hypes DOM management could/would collide (but I certainly would like to test it).
For a test I just used the MarkDown Editor Example from the VUE.js page and transferred it into Hype.