If you have the EndNote X7 or later installer, this is the command you can use to disable the automatic update check on startup:
msiexec.exe /i ENX9Inst.msi USERCANAPPLYUPDATES=F
msiexec.exe /i ENX8Inst.msi USERCANAPPLYUPDATES=F
msiexec.exe /i ENX7Inst.msi USERCANAPPLYUPDATES=F
This only disables the automatic prompt for installable updates once the application is started. It does not suppress the behaviour of the ‘EndNote Program Updates…’ menu under ‘Help’, which, when used, will always show the appropriate message. If that message is one controlled by the registry setting set during deployment, the download button will be hidden and the ‘Learn More…’ button will prompt the user to contact their site administrator.