I see #640 was just closed due to lack of a raised issue as I was typing this comment there, so I'm raising the issue for discussion first.
There is a bunch of discussion about the impact of the warning and the questionable benefits in docker/compose#11628. It's likely that the majority of users of docker-compose are not aware that the compose spec is a separate project - I wasn't until just now when I went to look at the history of this change.
I can see that the warning was first introduced in #575 and later added to the spec in compose-spec/compose-spec#489 - but it's unclear from those PRs how much discussion was had in other forums and whether the cost of creating warnings outweights the benefits vs simply ignoring the field.
These comments summarise the cost of introducing the warning and showing it to loads of people:
docker/compose#11628 (comment)
docker/compose#11628 (comment)
docker/compose#11628 (comment)
Are there large costs to retaining the version field but ignoring it that I've overlooked?