Personally, i prefer to keep those objects inside the container all the time, i.e. the container has a kind of process()-method that does the work on active ones and ignores inactives ones. If you store them in one list, iterate over them and do something if they are active or if you keep two lists in the container, one with all active, one with all inactive objects, is up to you. I usually prefer one list that stores them all, as long as this isn't a performance problem (what it isn't for just a few dozen objects).
I'm not saying that this is the best solution...it's just what i'm used to and what you can find in my sources (for example in the ParticleManager in the "advanced example" available in the download section).
Another solution: Make the container dumber and the objects more clever, i.e. let the container simply call a process()-method on each object and let the object do the work. This approach may be more OO, because it keeps work that belongs to a single object inside the object. However, it's not what i'm usually doing in games programming.