It looks like the roads you're talking about were the paths through every row of parking spaces. That's overkill, and you were correct to delete them.
In general, if they are large parking lots (mall, big box store, etc) go ahead and leave the roads. Waze uses them to route users to the store front. Roads along the periphery are ok, as are the roads leading from the traffic light to the parking lots.
To answer your other question, once you delete the segments, yes, you do need to delete the orphaned junctions yourself.
CM, USA/Canada ∙ iPhone 5 ∙ iOS 7.1