On the other hand: if these weapons can be equipped with microtransporters that can beam their bullets through solid walls to targets hundreds of meters away, they surely they could also beam ammunition into their magazines from some separate container stored nearby. Although that would require the fighters to stay within transporter range of the ammo reservoir, which might limit their mobility, depending on what that range is.
While that's an interesting idea, I must point out again that it would not be usable in the sort of dampening fields that necessitated the weapons' use in Destiny
, or that were needed to neutralize the Borg's adaptation advantage.
The problem with Trek tech is that it's easy to take it into such hyper-advanced territory that it can accomplish virtually anything, which is bad for storytelling. One keeps having to either devise arbitrary limits or just gloss over the potential applications.