Missiles are pretty much by definition going to be cheaper than similar speed disposable ships. Even if you want to accelerate the ships before launching, just do that outside the hyper limit; since missiles are essentially infinite ranged you don't gain anything by sending disposable ships in then launching.
This is one of those things I will have to puzzle out during game play. Missiles may be cheaper, but will have to be launched by something. I would rather send an expendable craft to draw fire and locate future targets than risk a more expensive, dedicated missile platform.
It will also depend on how effective anti missile defenses are. If the parasite can provide decent cover for the missiles during part of their time to target, then this could be a bonus. With rail guns and a laser it may also be able to engage some defenses that are identified. How successful it will be is yet to be seen.
How the game's dynamics will work will shape a lot of the tactics. If missiles can reach enormous velocities from a slow ship, and missile defenses are poor against that target, a pure missile attack from long range may be good.
Since I don't have a clue how it will work, my first plan will be to test the waters with craft that are fairly 'expendable' and armed with a variety of weapons. I like the missiles versatility and payload. I like the rail guns lethality in what I assume will be a nearly invisible and difficult to stop package. I like lasers as a nimble target will still find itself in trouble against them - and they don't run out of ammo. So I would go with all of them and see what my opponent finds hardest to counter.
And if he does counter all of it - I'm only out a bunch of 'expendable' craft. Granted it will be more expensive than missiles - but hopefully they will also have identified more targets and weaknesses than a single form attack.