I have read that DLCs can't reference each other, like how Grunt from HH does not effect the bowie knife from LR.

So why can I purchase .45cal ammo from the vendor in LR?

The vender used in LR uses more then one vender list of items, some of which were also altered by HH, so if you have HH loaded along side LR, then LR uses those altered lists. There is no trickery or secrecy here. LR does not reference HH in any way.