I have tested the site and with WPML, the default language home page is set to Yes to index in the backend but when viewing the source code shows: content='index, nofollow
I then enabled WPML and tested with this page: hidden link which is set to Yes to index and on the source code, I see content='index, follow'
I next edited the English translation of this page and set index to No in the advanced yoast settings. When I view the source code for hidden link I see content='noindex, follow'
So, it appears to be working as expected but not on the homepage. However, even with WPML deactivated, I am not able to change the index status of the homepage using the settings in the page editor. So I think for the homepage, the issue is coming from somewhere else.
If there is a page other than the homepage where you are still seeing the issue, please let me know and I will be happy to further test.
