Hi Craig,
I'd be interested in producing a custom extension for this problem. My way of approaching the problem might be slightly different from yours though (depending on whether inkscape stores the circle centrepoints and radii for a collection of merged circles, if not it might require that the circles are not merged before the extension is installed).
If I understand you correctly the solution you have in mind would require the outline to be a composition of circles. However, I can imagine many other use cases for this kind of request in slightly different circumstances where the outline is a general path (and the items to be counted may be arbitrary objects). Even though he implementation seems easiest at first if you restrict yourself to circles, I would very much recommend not to make any assumptions to that effect and keep the functionality as generic as possible. Of course it would be overkill to implement a test whether an arbitrary path contains another in your extension code, but have a look at lib2geom [1], the geometry library underlying Inkscape. I haven't checked recently but it might contain functions to test wether one path lies with the boundaries of another (or at least whether a given point lies within a path, which might already be enough for your purposes if you only take the centers of the small red dots into account). If it doesn't, this should definitely be implemented anyway. :) The libary also has Python bindings.
On a different note, instead of counting the items within the outline path directly, it might be better (as in: give more flexibility for other use cases) to provide an easy way to *select* them. See my comments on the bug report: https://bugs.launchpad.net/inkscape/+bug/621627
Hope this helps, Max