The server needs to reboot to finish patching files that were in use during the patching process, leaving your machine in an inconsistent state (IE installing updates and then letting it run) leaves your machine at greater risk as you are between two states.
The first before you patched as a known good level of Microsoft updates.
The second state is your machine running the latest set of Microsoft patches.
What you are creating is a third state where some files are updated whilst others aren't, the question isn't really are you more at risk (Because the answer seems an obvious yes) its what steps would you take if your machine was comprimised during this inconsistent state? I would imagine Microsoft would say to you what they said to me in the past 'Oh dear I'm very sorry, rebuild your machine it wasn't in a configuration we support'
If you're patching your machine do it in one hit, apply the patches and immediately reboot it - even if it means staying around out of hours to do it. If your application is that critical that you cannot manage a 5 minute reboot outage then you ought to be looking at extending your infrastructure to cope with it (ie: Multiple load balanced servers).