ShellSettingsManager enables you to access and modify Visual Studio settings but only in the Windows registry. Any changes you make will not be picked up by Visual Studio until it is restarted because VS reads settings from the registry only when it starts. So this is the wrong approach.

To both change settings and apply them without requiring a restart, you will have to use DTE2.Properties as discussed in here. The following code snippet shows all the settings that can be changed programmatically from the Environment/General page (this is where you can change the theme):

EnvDTE.Properties generalProps = dte2Obj.Properties["Environment", "General"];
for (int i = 1; i <= generalProps.Count; ++i)
{
    System.Diagnostics.Debug.WriteLine(
        generalProps.Item(i).Name + ": " + generalProps.Item(i).Value);
}

By default in VS2013, this code will produce the following output:

AnimationSpeed: 5
RichClientExperienceOptions: 65535
WindowMenuContainsNItems: 10
CloseButtonActiveTabOnly: True
UseTitleCaseOnMenu: False
AutoAdjustExperience: True
Animations: True
AutohidePinActiveTabOnly: False
ShowStatusBar: True
MRUListContainsNItems: 10

All of these settings can be changed and VS will immediately apply the changes. The problem is that there is no property that enables you to change the theme. That's why I think it cannot be done.

Here's the simplest way to do it:

Overview:

1. Use the "Import & Export Settings" feature to create two files: DarkTheme.vssettings and LightTheme.vssettings
2. Programmatically invoke the Tools.ImportandExportSettings command to import those files at the appropriate time.

Details:

To create the two settings files:

1. Launch Visual Studio and set the theme to "Light" through the UI
2. From the Tools menu select "Import and Export Settings..."
3. In the wizard, select "Export selected environment settings" and click "Next"
4. In the "Which settings do you want to export?" page, deselect everything except "Options/Fonts and Colors" and click "Next"
5. Name this file "Light.vssettings" and save it in a known location.
6. Repeat steps 1 through 5 for the "Dark" theme, naming the file "Dark.vssettings".

To import these files programmatically use DTE.ExecuteCommand with the "/import" parameter like this:

Add a reference to EnvDTE.dll if you don't have it already.

var dte = GetService(typeof(EnvDTE._DTE)) as EnvDTE.DTE;
dte.ExecuteCommand("Tools.ImportandExportSettings", @"/import:""C:\yourpath\LightTheme.vssettings""");

I hope that helps.