Not documented on their site, but it appears to be an InnoSetup installer. To suppress the Install/Uninstall progress window, use /verysilent instead of /silent
Install:
setup.exe /silent /suppressmsgboxes /log="C:\Windows\Temp\install.log"
Uninstall:
"C:\Program Files\Wolfram Research\Mathematica\9.0\SystemFiles\UninstallFiles\Windows\unins000.exe" /silent /suppressmsgboxes /norestart /log="C:\Windows\Temp\uninstall.log"
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