I have never used Worldkit, but MODx can of course handle Flash stuff easily.
Worldkit uses XML for its data-source. It depends if you want to edit those XML files directly within MODx*, or if you want to generate dynamic XML from MODx-containers and -documents**. But both is possible.
* use regular modx-documents, set content-type to text/xml (2nd tab in edit-mode).
Point your Flash-movie to the modx-URL.
** For the actual data (XML nodes/attributes) create a special template + template variables (TVs).
Put all data that generates a map into a separate modx-container. Each child-document holds the data for each map-point / location.
Use Ditto to generate the XML (one snippet call per container = map).
To make it truly dynamic, add the XML path via TV:
fo.addVariable("dataurl", "
http://www.example.com/index.php?id=123"); // Check the docs:
http://worldkit.org/doc/dynamic.php
That way, you’ll only need one SWF for all maps and you don’t need to publish a separate movie for each map.