There are already plugins (OK, one at least) and individual plugin tweaks that enable you to DISABLE plugin update notices, but 'DISABLE' and 'DISMISS' are not the same thing. If you disable updates, either for individual plugins or globally, you're basically saying never ever tell me again that updates are available. If you could dismiss an update, you'd be saying 'OK, acknowledge that it's available but I don't want to install this one'.
I would imagine it wouldn't be difficult to do - either as a plugin or as a 'tweak' to core code. WP obviously already checks a site's currently installed plugin version number against the latest available one ... just needs to save the latest version number somewhere to tell the system it has been notified (and dismissed).
Unfortunately my knowledge of plugins is limited to 're-engineering' existing ones to tweak them to my purposes so I wouldn't dare try to write it myself, but I'm sure I'm not the only person who would find such a facility really useful!