An NDAA passes regularly to fund the armed forces, including benefits for veterans etc. Every President in recent memory signed a bunch of them. That's not comparable to CISPA
Also, the brouhaha over that bill is over how it might be interpreted in a parallel universe where Hamdi v. Rumsfeld doesn't exist.
As the President cannot veto part of a bill, vetoing the NDAA over those provisions would literally mean vetoing the entire defense budget.