It's funny that you picked this as an example, because the 2nd ave subway has yet to open even it's very short initial segment, and the 4-5-6 (Lexington Ave line) is the least redundant part of the whole NYC subway system. It's the only north-south line on the East side, and it carries more people per day than the entire subway system of any other North American city.
Once they build out the 2nd ave subway to the bottom of the island things will be redundant...but that's decades away. (They won't even start construction on the second phase, which only takes it up to 125th st, until 2020.)
You point generally applies to the rest of the system, though.