I support with your decision.
After reading some articles about plutonium, I have found that "depleted plutonium" (abbreviated as DP below) is not a suitable material to be used for ordinary ammo like what depleted uranium (DU) can do.
Pu-238 (which represents DP in your mod) does not have any outstanding physical properties, to warrant the extra ammo damage over the vanilla DU ammo. Combined with the fact that it is so scarce compared to DU (in both your mod and IRL), it has little incentive to be used as DP ammo. So taking this away (completely or as setting) would be a good decision.
The much more useful property of Pu-238 is its radioactivity (alpha radiation). Its main usage IRL is RTG.
However, the game already has the all-powerful and ultra-cheap portable fusion generator giving lots of energy, leaving little place for RTG. (Unless you provide an new option to disable vanilla fusion generator, so forcing them to use Pu-238 to craft RTG? That would be another story.)