Building some bunk beds that will be pretty permanent and my plan was just to glue everything to make it nice and sturdy. If I'm gluing is there any reason to use screws at all, trying to make it look nice?
Lee's comment is right on Ryan. But in any case, we couldn't answer your question without more detail about the construction. Depending on what you're planning, even screws+glue might not be strong enough.
In particular, glue is only strong in shear, and not tension. It's also not effective on end-grain. With either screws or glue (or both), you'll still want the mechanical strength of the wood to be working for you, and that will mean non-trivial joints like mortise and tenon. Just butting pieces up against each other and joining them with glue and screws risks ending in tears.
A bed especially is subject to jumping and climbing stresses and has unconscious occupants much of the time.
If you can provide drawings we could give you something more specific. If it were me, I'd be thinking hard about a quick trip to IKEA :)