The interfaces you delete won't come back in discoveries unless you delete and re-add the whole node. If you have your discoveries set up to run every day and you tell them to import only new things, it will only show you new nodes and the interfaces associated with those new nodes. It won't show you "new" interfaces as in the old ones you've deleted. I've never had a problem with it adding back interfaces I've deleted onto a node that already exists. If you want to add the interfaces back, you'll have to click list resources on the node and select them back there. You could also do another discovery where you say to return all results, not just the new ones. That would add the interface back there if you have it selected.
Unmanaging an interface just keeps it from collecting statistics every however long your polling interval is. So it still counts against your total elements.