The plugin have an option for notes, please try this. You find it in the global options area of the settings page.
Thanks, but I’ve already checked and it doesn’t work for plugin notes.

OK, maybe the plugins don’t use the default notes. But you can add custom options to the global options. Find a selector of the notes, like the ID via Webinspector and add this to the custom options.
This notes don’t have the ID, they have a class, such as:
<div class=”error”>
<div class=”updated”>
Can I use it in Adminimize?
You should add the classes to a custom option, like .error and named like ‘Error Notices’. Also for the update messages from plugins .updated, named maybe as ‘Update Notices’.
But be aware, this remove all notices with this classes.