Suppress HttpException.404 for bad URLs
The good news in the upcoming Craft 3 this isn't an issue.  404's get logged to their own separate log files and won't clutter up the main Craft log files specifically for this reason.

In Craft 2, I think you'd have to do something like write a plugin that listens for Yii's onException event, makes sure it's a 404 status code, then go through Yii's CLogger to get the full list of log entries and remove the last one.