Weghorst was definitely used correctly by Koeman, the problem is Memphis. He has been very useful for the Netherlands, scoring lots of goals, but he really seems to be fading now. It's understandable that Koeman sticks with him given Memphis's past record, but by always playing Memphis and never Zirkzee or Brobbey (or even Luuk de Jong), Koeman created a situation where there's no backup for Memphis's role (which Weghorst can't play) with any real experience in playing for the Dutch national team. Consequently, when Memphis was pretty useless during the EC, there wasn't someone who could really be trusted to be the starting striker instead.
But yes, many people in the Netherlands did think that someone should have been Zirkzee, and except if he tanks at United, I'd be surprised if Zirkzee didn't start getting more game time in the Dutch national team soon.