What is the difference between a secondary weapon that says "spend your target lock and discard" vs something like Homing Missles which still says "Attack (Target Lock)" but does not actually says to spend the token and discard? Why is it still a target lock thing?

Because Attack: X doesn't mean 'spend X to attack' it means 'have X to attack'. The token is only spent if the weapon specifies that it is spent.

Homing Missiles still require the target lock on the target to fire them. They just don't require you to spend it.

Because you don't have to spend the lock to perform the attack, you can then spend the token to fettle your dice rolls.

Which is why they don't have any 'innate' dice modification like, say, concussion missiles (which give you a single blank-to-hit to make up for the target lock token you now don't have for rerolls).