That makes absolutely no sense. I've played hundreds of PC titles and I've never seen one that hides your saves in a hidden and obscure directory.
For reference, the folder is actually C:\Documents and Settings\username\Local Settings\Application Data\Ironclad Games\Sins of a Solar Empire
Actually, as a Windows dev myself, one of the biggest reasons why stuff is saved to this folder (often called the APP_DATA directory by my colleagues) is more likely due to permissions. This is true since XP, so it is less likely to do with "Games for Windows" policies and Vista.
In normal XP with multiple user accounts, it is default that applications do not have read/write permissions to almost any place, including its own directory. This is why you often hear instructions that such-and-such app must be installed as Adminstrator. The only place that by default allows read/write permissions is in the specially created APP_DATA directory for each application. If an application dev wishes to have R/W permissions elsewhere, then special setup/configs are needed at install time (see install wizards, NSIS, et al). This can be a big hassle to do for an installer. And it can clash with other security policies that may be in effect at the time.
The only other location for an app to save its own files is %TEMP% which clearly is not suitable, and the "My Documents" folder, which is probably already heavily overused. Besides, My Documents usually shows up in most applications' File > Open, so for an application to save app specific files which do not really need user access (eg. logs, saved data, etc), APP_DATA is the usual place.
So, just for reference in XP (this is true for most all standard Windows apps):
C:\Documents and Settings - Windows installed default
<username> - in case of multiple accounts on the same PC
Local Settings - to force data to be local, as opposed to roaming user profiles in Windows
Application Data\IronClad - self-explanatory
In Vista, it is the same, except that they merely moved folders and names around.
I just wanted to explain this so that people have a better understanding (a likely reason) why IronClad did this - to improve compatibility across all Windows installations - and not because they decided it on a whim 