With iOS12 the emoji key has been switched with the number/punctuation key. Is there anyway to move them back so that the number key is under the capital shift key, instead of the emoji key?

There is absolutely no way to change this. This is a fixed UI element.

It is part of iOS 12.

Know one, but Apple, knows why they decided to change the position of these keys.

If you do not like this change in iOS 12, you can complain to Apple via their feedback page here.

iPad Feedback

http://www.apple.com/feedback/ipad.html

You, also, have the option of seeking out another third party software keyboard from the iOS App Store, as well.

iOS 12.0.1 update released yesterday : About iOS 12 Updates - Apple Support

Restores the original position of the “.?123" key on the iPad keyboard

No, not unless Apple change it an update. If you want to leave feedback to them about it : http://www.apple.com/feedback/ipad.html

and in ios 12.1 it has again switched places :-( and I hate it. it hurts my stomach everytime I press the wrong key

they bug fixed this with 12.01 the obviously didn’t add it to their test cases so it appears again In 12.1. The question is.... will they fix it again. It’s so annoying.