This decision applies if you are using a Langstroth hive only. Using medium or deep frames is just a trade off and either work just great. Although all sorts of combinations exist, two common configurations for a hive are two deeps or three mediums. You can mix and match, though, if you want. The deep box can obviously hold considerably more honey (or brood), but that comes at the cost of more weight to lift at inspection time. It's really down to you and you are not making a mistake with either. It's just a question of weight vs. capacity.