I'm not saying you will switch a lot between them, i'm saying that if you upgrade Hercules weapon (for instance), it won't help any solomon when you are using her during the early tower. Upgrade an assault weapon will. I'm not saying it will do a tremendous difference because you should switch as soon as you encounter difficulties anyway, but i'm just saying it's another thing to take in account.
Edit: To be perfectly clear, of course you should upgrade your soul weapon. However, in this specific case, with limited ressources and especially R weapons, soul weapon is not always the best course of action, especially if you still have a lot of SR assault in your grid. That's all.