If high CR monsters have magic items in their starting equipment I have added the item as a description added to the relevant area e.g. if the the monster has +3 breast plate, a text of +3 breast plate will be added next to the AC line.
A +3 warhammer will be added next to the Attack line.
The magic bonuses are not added into the stats though. You can add in the magic equipment by adding it into the magic items list and recalculating, or just manually add in the bonuses.