If you wish to install NX Client or the NX Add-On fonts without having any windows shown during the installation, you can choose to use the silent or verysilent switch.
For example, you can run from a DOS shell:

>nxclient-3.5.0-9.exe /silent

or

>nxclient-3.5.0-9.exe /verysilent

When using the /silent option only the progress window will be shown while with the /verysilent option no window will be shown at all.

If during the upgrade, the installer detects that at least one NX Client component is in use, e.g. because there is a NX session running, it issues a dialog message:

NX Client for Windows detected that some programs are in use by Windows.
The setup will not be able to replace these file. Do you want to kill the running programs?
 
If you have a NX session running and you accept to kill all the running programs, you will be able to reconnect your session later, as soon as the upgrade has been completed.