You should listen to it, especially if you’re a plugin developer.
Deactivating and uninstalling a plugin are not the same thing
Let’s talk about plugin options. Specifically, what I expect as a user when I deactivate a plugin, versus uninstall one. WordPress has some hooks built in that help enable plugin others to do things, namely register_activation_hook, register_deactivation_hook, and register_uninstall_hook. The deactivation hook and uninstall hook are great places to trigger certain things. Unfortunately, too many plugin authors unset options in the wrong one.
When I deactivate a plugin, I’m not really trying to totally remove the plugin from my site, but rather just turn it off. So when a plugin author deletes all of the options I’ve selected on a plugins’ settings screen on the deactivation hook, it makes me angry that I have to go and reset them when I turn it back on. So angry that I might just find another solution for what your plugin is doing.
What they should be doing instead, is removing these options, and everything else, with the uninstall hook. When i uninstall a plugin completely, it is safe to assume I am finished with it, and it is the appropriate place to take such action. But when I simply deactivate, in all likelihood I’m just debugging something in my theme or another plugin, or maybe backing up or upgrading something.
So consider this a friendly message to plugin developers, and future plugin developers – remove options on the uninstall hook, and not the deactivation hook.