I actually haven't had any problems running it like that. I'd had a lot of problems with earlier versions, but after the recommendations of somebody here on Interact, I gave it another try. So far, I like it.
I'm not sure if you can make it out, but you can see that Sysmetrix is reporting my uptime as over 4 days in that screenshot. I had to reboot after installing DesktopX and haven't rebooted since. Believe me, if the system starts to feel unstable, all the pretty stuff will go away. I treasure stability over beauty when it comes to my PC.
I actually read an article where some guy ran 3DMark and some other benchmarking apps and games on his PC after a fresh format\install of Windows and after installing and turning on all the stardock apps. His scores were either the same, or only a frame less per second. Pretty interesting. I originally had my PC configured with one account that I do most things from (the one in the screenshot) and another that I game from that only loads what's absolutely necessary. I may change that now, though after reading that article.