Is it safe to leave powder in hoppers? Or should you empty the hopper everytime you use it?

By powder in the hopper, you are referring to the powder reservoir in the powder measure? If so, yes you should empty the reservoir when you are through charging your cases and return the unused powder back to its' canister.

A shooting pard of mine used to leave his powder reservoir partially full without any problems after he reloaded. His reloading bench is in the garage and eventually moisture got into the reservoir causing the powder to "bridge" e.g. form a solid layer across the reservoir. Powder below the bridge flowed into his cases but powder above did not. Unfortunately his didn't find out about this until he was at the range and some of his rounds went "poof" instead of "bang". Now he was stuck with the dilemma of which cases were charged and which were not? This led to pulling bullets and reloading all over again. Fortunate that he found out about this at the range and not when things "go bump in the night".

Some powders like Bullseye will stain and/or pit the plastic reservoirs on some measures.

Argo is right. High NG powders can actually dissolve the reservoir over time. There's also the humidity factor, which doesn't help. No, ALWAYS return the powder to the canister - hopefully the one and only canister you have on your bench so that it's the RIGHT canister as well!

Thanks for the info

As lightly touched upon by Rocky Raab, a very good reason to return the powder to the proper can is to make sure that you never mix up the powder that is in the measure. Unless you are only loading one powder, ever, the possiblity exists that you might forget what is in the measure and add the wrong powder, or pour it into the wrong can when you need to switch.
Better safety practice and better housekeeping all around.
If I am loading a large batch of ammunition over several days, I might leave the powder in the measure. When I am finished, it goes back into the container.