Do you _only_ use virtual folders?

Currently I have it set up so I press a shortcut that takes me to a virtual folder for my inbox. I'm not sure why I don't just by default only use virtual folders. I think the reasoning is I was concerned that if I deleted a message I wasn't sure whether I would delete it from my inbox or a different location that was made available because of finding the thread. I don't know if this is to be a legitimate concern or not. Is there a reason not to only use virtual folders? Do you use virtual folders by default or do you only switch when you e.g. want to open a thread? Kind regards, Xu