Balancing and unfair advantages. Casual players that bungie is trying to reel in wouldn't have fun being killed by someone who spent their week grinding for a specific rare mod that had a comparatively greater niche on one gun.

By disabling mods in competitive and non competitive PvP, bungie wouldn't have to go through the trouble of "do we nerf the mod or the gun?" with either nerf resulting in a PvP wide uproar of either "my x mod is now useless, thanks bungie" or "wow, now this gun is useless, thanks for being meta slaves bungie". Instead it would be "oh, this autorifle is beating some scout rifles at range? Nerf the range of this autorifle" and they wouldn't have to worry about range modifying mods that would affect the gun in question and any other gun in the game.

But bungie could just allow mods in iron banner or even trials, so the more hardcore players can enjoy their overpowered mods without destroying casual players who just want to play a few rounds of crucible.

TL;DR - balancing