Should there be waterproofing between the rim joist and ledger on new construction?
You do not need water proofing in between the ledger and the rim joist, but the joint needs protected some how.  Flashing, roofing membrane, etc.  And what ever it is needs to go under the siding and over the ledger in a continuous fashion with no seams at the ledger.  Tar paper is not enough.  Metal, EPDM, etc is what is needed.