Timeline issues. Perez's Wonder Woman(late 80s) was supposed to be a reboot of the character ignoring the character's existence before that(though keeping some of the same elements). So at that point it was essentially being treated as 'Wonder Woman didn't exist in the DCU pre-that period in time'. It wasn't until Byrne(mid-90s) that the storyline of Hippolyta being Wonder Woman during the War and the time traveling thing was brought up. So in that regard the characters in the 80s/early 90s comic didn't acknowledge 40s Wonder Woman because at that point in time it hadn't technically happened yet.