Running a screensaver consumes processor power that could be better put to use to run SETI. My personal preference (and recommendation for others) is to set your system to use no screensaver at all, but instead set up the power saving options to shut down the monitor after 15 minutes or whatever. Also, be sure that your hard disks are set not to power down, because your distributed computing program needs to be able to access them.
Edit: Ok, I see some misunderstandings here... I'll try to clear things up.
Whether the monitor is on or off does not matter to the computer. Your graphics drivers use DDC to get info on screen size and supported resolutions when your OS goes into graphics mode for the first time, but other than that, AFAIK, communication between your computer and monitor is a one-way ordeal. Hence, having or not having a monitor connected and/or powered on does nothing to affect the speed of anything on your computer.
Running a blank screensaver won't make anything faster than it would be otherwise; all it will do is prevent background tasks (e.g. SETI) from being slowed down. Now, in the case of SETI, the CLI is much faster (or, more efficient) than the GUI, for reasons that are beyond my understanding. This does not necessarily hold true in all projects under all circumstances, but that could get confusing so I'll stop for now. 🙂