The timeline's always been a mess, but it has been something that has been given serious thought since at least the late 90s.
https://www.zeldadungeon.net/forum/threads/the-truth-behind-...
https://old.reddit.com/r/truezelda/comments/sejcwx/newly_tra...
https://old.reddit.com/r/zelda/comments/6866wt/addressing_th...
That's not to say that there is a capital C canon that constrains all subsequent installments to be 100% self consistent. They seem to enjoy the freedom of being able to change things to fit their vision for the next installment. I just don't think it's correct to say there's no thought at all put into the head revision of the canon.