It's *real* problem, although a minor one ;) Basically with a few small changes in the core we can achieve small performance gains on all pages by reducing CSS that is never used. It's not going to crash or anything but the process is flawed - it's been around since DNN 1 and needs a revisit, especially now that Google ranking takes into account page speed...

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Yes, but how are we going to get Microsoft to combine all the ajax js files, and actually get them emitted with an expiry date on them instead of each being dynamically generated?

I've looked into the core code, here's the bit that does the module.css output:
' 1.try to load module.css from module folder
                    If File.Exists(Server.MapPath(Common.Globals.ApplicationPath & "/DesktopModules/" & folderName & "/module.css")) Then
                        objCSSCache(ID) = Common.Globals.ApplicationPath & "/DesktopModules/" & folderName & "/module.css"
                    Else
                        ' 2.otherwise try to load from Path to control
                        If controlSrc.ToLower.EndsWith(".ascx") Then
                            If File.Exists(Server.MapPath(Common.Globals.ApplicationPath & "/" & controlSrc.Substring(0, controlSrc.LastIndexOf("/") + 1)) & "module.css") Then
                                objCSSCache(ID) = Common.Globals.ApplicationPath & "/" & controlSrc.Substring(0, controlSrc.LastIndexOf("/") + 1) & "module.css"
                            End If
                        End If
                    End If

As you can see, there's really no way of changing or overriding this, because it is explicitly searching for the module.css file either in the module path, or in the same path as the .ascx file.  You could theoretically hack this process by locating each .ascx file that didn't need a common module.css into it's own directory (ie /admin/ for the admin files, /view/ for the 'view' modules) - as long as you don't include a module.css file in the root path of the desktopModules/modulename directory.  I might have a look further at this technique.