Yes and no.
If you don't play the metaverse then there is no problem.
If you want to play metaverse games then there is an issue but it can easily be fixed.
When you install SDC it records your serial number (actually two serial numbers one for DL and one for DA) in the registry under the HKLM/SOFTWARE/STARDOCK key.
When you uninstall SDC is deletes these serial numbers. If you don't play metaverse games then it doesn't matter because you can play the game just like normal. However if you want to submit a metaverse game then you can't because of the deleted serial number.
However, this is easy to fix. All you need to do is *before* uninstalling SDC you goto the Start Menu and click on "Run" and enter "regedit" (without the quotes). This brings you into the Registry Editor. From there you can scroll down to the HKLM/SOFTWARE/STARDOCK key and highlight it and then goto the File menu and click on Export. This will allow you to save a .REG file which will allow you to restore the exported key after uninstalling SDC.
Just in case you're unfamiliar with the Registry HKLM is short for HKEY_LOCAL_MACHINE. Anyway save the file to something like Stardock.REG. Then once you've uninstalled SDC you can just double click on the Stardock.REG file and it will restore the serial numbers to the state they were before SDC was uninstalled.
You could also go back into regedit and do file/import as well.
I do the same thing but not because I care about 80MB on my 240GB hard drive but simply because it's an overly complicated piece of software that does a whole bunch of things that I have no interest in whatsoever other than occasionally updating GalCiv2 which is a piece of software that I do care about.
Hope this helps you because I found this out the hard way when I finished a gigantic game that scored 872K points and couldn't submit it.