If nvultra (running Version 1.0.0 (39)) is set to show only a menubar icon (Preferences > General > Behavior, then it will disappear when invoking hook (I use the default key strokes Shift-Command-Space)
if the behavior is to have a menubar icon AND a dock icon, then nvUltra stays open when the hook window opens …
I can replicate this with and without using Hook. Spotlight and LaunchBar don’t cause nvUltra to disappear. Disappearance seems to be triggered by running the AppleScript. I can replicate it without Hook by
invoking nvUltra window
using spotlight to run an app compiled from Script Editor that includes a line of AppleScript that interacts with nvUltra