While using module_invoke for things other than hooks today, I do not think we should recommend it since the purpose of module_invoke is to invoke the hook. Using module_invoke for more than its intended purpose is confusing and may cause issues in the future should module_invoke change its ways. Module_invoke is more like calling an object function while executing the function directly is more like executing a static class function.
Earnie
For what it's worth: Drupal's core API changes only between major versions. As long as we're speaking of D5 and D6, and of contrib modules for D5 and D6, I would repeat my previous recommendation to a) remove unnecessary module_exists()/function_exists() code bloats, and b) manifest a best practice that can be dealt with in the module upgrade docs for D7 and/or beyond. Until there is not a better API method, it is absolutely safe to use module_invoke(). Look, it's still there: http://api.drupal.org/api/function/module_invoke/7 Daniel