The cache plugin compatibility problem is caused by those cache plugins that save whole Wordpress pages as html. These plugins can block WassUp's tracker function from executing each time a cached page is displayed and cause the number of visitors to be under-counted in WassUp. This has been the case since the earliest versions of WassUp.
For a statistics program, having underreported data is unacceptable, so that is why there is a notice about cache plugins in the ReadMe instructions and now in a install/upgrade alert message (since WassUp 1.8).
That said, not all cache plugins are the same. If you have one that doesn't block WassUp or if you were satisfied with the data that WassUp generated for your site in the past, then you should keep using WassUp (1.8.1) with your cache plugin despite the alert.
If you want to switch to another cache plugin, read WassUp'd FAQ at http://wordpress.org/extend/plugins/wassup/faq for a list of compatible plugins. If you know of one that is not on the list, please tell us here.