That's sort of what the "Number to: Rename Component" option is for. When this is set, whatever numbering setting you use will change the name of the component instance instead of placing 3D text. Then in Layout, you can use the label tool with the Component Instance option. This will give you the text created by Number Components in SketchUp. This could still involve an awful lot of clicking, but the numbers will be there automatically.

For example, you could select all your windows, use "Text n" and set the prefix to "Window ", "Number to: Rename Components". Then in layout, just click on each window with the label tool and you'll get "Window 1", "Window 2", etc. for the text.

There's a Ruby API for Layout now, but I haven't looked at it. It's not interactive so the plugins don't run in Layout. It might be possible for a plugin to create a Layout file with the numbers labels all arranged automatically, but I don't know.

Number Components 1.1.2 is now available to download on SketchUcation here:

Number Components

This plugin numbers a selection of groups/components by placing 3D text above them. Can number them sequentially with various options for direction of numbering and text prefixes. Can also replace component's instance names with numbers.

Usage
Select some groups, components or a mixture of the two types. Set the view to either Top or at least to be looking down on your selected components so you can see the results of this plugin.

Right-click on your selection, then choose "Number Components" from the context menu that pops up.

Choose from the following options:

Font, style, text height, extrusion size (0 for no extrusion), unit (mm/inches), direction, Numbering system, Text Prefix("Text n" only), Number to 3D text or rename component ,First number, Flip alternate rows, Keep window open.

All settings are saved to disk so they should stay at your last used settings even after restarting SketchUp. Note that they have to be used by clicking the "Number Components" before they're saved to disk.

Click 'Number Components'.

Updated youtube demo of Number Components with font support: