Should a module implementing a filter delete the Drupal variables it uses, when uninstalled?
A module should be responsible for cleaning up after itself when it is uninstalled. There is no reason not to do this, unless some other modules depend on those variables but I very much doubt this is a case. If they depend on a module they probably depend on the entire module, not just some variables defined by it.

I, for example, use htmLawed and out of curiosity checked the .install file; it does clean the variables defined in the format "module_name_format_%".

As a best practice you should drop all the tables and delete the variables defined by your module, doing this by implementing hook_uninstall in your .install file.


Writing .install files (Drupal 6.x)