It will connect to all 100 if you deploy it to the same EminentWare Computer Group. However, if the rules are properly configured for the package, the WUA on the 50 that already have it should evaluate the update as either Installed or Not Applicable. So, there might be some traffic/connection to those machines, but they shouldn't have the update reinstall.
Another Option: A new Update Management task can be launched from results dialogs. In the Task History item for the previous deployment, go to the Details tab and sort or group so that you can multi-select the computers that were previously offline, then right-click that selection and choose "Update Management". You would then need to click "Select Updates" and choose the particular update you want to deploy.