Well beyond the more serious ramifications of what will happen if you make a mistake, there are many other fundamental differences.
While you are basically correct, the technique should be the same, with or with out a weapon, whether the technique will ever arise or not is another thing. Yes a shihonage is going to be a shihonage, whether you have a weapon I have a weapon, or neither have a weapon. But will you have the opportunity to use a shihonage?
In unarmed fighting the fighter can choose to go to the core of your body in order to control you. This is the superior way to control a person; by going directly to their core. Things like Body locks, waist locks and headlocks are superior positions. The reason they are superior is because they are a quicker and more direct means to control what you need to control in a physical confrontation; the core.
These means of control being superior, if you attempt Aikido techniques while unarmed against a trained unarmed fighter, they will likely win. They will be better from the superior position (we don't train said techniques).
So what changes all of this? A weapon. If someone tries these superior unarmed techniques (body/headlocks) on you while you are armed, they will be neglecting your limbs. If you are armed, they will lose (weapon will win even in a bad position). Now if they take your limbs into account and try to hold them...we have shihonage; or any of the other techniques of Aikido.