Indeed, it looks like package has not been rebuilt for latest version link.
Yes, installation from source should be straightforward. It needs Qt5.5 (0.6.3 worked on Qt4).
Quick compilation guide below, (details are in readme).
git clone https://github.com/Nitrokey/nitrokey-app.git --recursive
#install is optional - needed only for udev rules to be copied, could be done manually too
Edit: just checked and the issue is not occurring on v1.1, Ubuntu 16.10, Storage v0.45 - clipboard was correctly cleared.
Edit: without udev rules (allowing to use USB devices by user) it might not be possible to use the Application without root privileges