My 5e group has reached level 5 and all have acquired +1 weapons. This renders the monster ability of "resistant to bludgeoning, piercing and slashing damage from non-magical weapons" a moot point. It's possible they'll wind up in circumstances where they need to use improvised weapons, but for the most part, this monster ability isn't going to affect play.
This is unlike resistance to Fire or Lightning, in that those resistances don't go away when the players acquire gear.
The Effective Hit Points Based on Resistances and Immunities table (DMG 277) provides a multiplier based on monster CR, but doesn't address party level, which is a pretty strong indicator of the likelihood of the party having magic weapons.
Should I continue to use these now-moot resistances when calculating effective monster HP for purposes of determining CR?