On opening a new tab window height does not update/change automatically which causes lines at the bottom (specially vim status line) to basically vanish. The window resizes if switch between the tabs. Also on closing a tab windows height does not change and causes everything to move up a few lines.
Here's a GIF showing what happens:

Yep, I see exactly the same behavior on Windows 10 with the latest Canary build.
Exists in v2.0.0 and latest canary (v2.1.0-canary.2) aswell. I can even confirm that it exists in vanilla Hyper with no themes or plugins installed.
I'm using Ubuntu 18.04, so I guess it's OS-independent.
I'm having the same issue on debian with hyper 2.0.0, also, when I close a tab, keeping only one tab, the height of the window stays the same, as if the tab still exists.
This seems to have been fixed in version 3.0.2, on my machine at least (Arch Linux). I am closing this issue assuming it has been fixed for everyone else as well.
confirmed to work on Ubuntu Pop!_OS
Confirmed to work in both Ubuntu Budgie 19.04 and Windows 10.
Most helpful comment
Exists in v2.0.0 and latest canary (v2.1.0-canary.2) aswell. I can even confirm that it exists in vanilla Hyper with no themes or plugins installed.
I'm using Ubuntu 18.04, so I guess it's OS-independent.