The distinction is that reconnaissance/espionage can be done quietly without destroying any hardware or disrupting data integrity, and it's far more difficult to pinpoint who is responsible for offensive/exploitative network operations. The number of organizations across the world that have nuclear capabilities is quite small, however the number of those with offensive security operations capabilities is quite high. The anonymity provided by the depth of the internet is a double-edged sword.

Furthermore the splash damage from Stuxnet/Flame is a testament to the distinct lack of surgical precision normally afforded by missiles.

Also, zero-day exploits can retain their usefulness even after it's been deployed, meanwhile a missile is gone when deployed.