Game version: Steam Stable Alpha - 0.5.102571
I see no reason why inventory system and other containers like ammo boxes and vehicles should not behave as when on dry land (other than techinical issues I might not be aware of). I understand such limitations might have been ok in Arma 2 where you could potentially destroy vital mission gear by discarding items while swimming.
Enabling full inventory control while swimming and diving could be beneficial for objectives such as retrieving items from underwater containers, dead bodies or sunken vehicles and would certainly benefit the user experience by having such actions done in a consistent manner no matter the environment.