Is this the first think before making any modification to any element that could affect the layout or is there something that I'm not aware of to prevent from taken these elements out of the normal flow?
Sorry if my question doesn't make too much sense!
There is nothing that prevents you from hiding, animating, etc. crucial elements in your page's DOM. These decisions are left up to you. As a note, these elements are still present within the page---unless you explicitly delete them---so you can always restore them need be; for example, hide x until the user does y.
Therefore, it is crucial to think of any consequences of DOM modification when laying out a page's markup. For example, it may require wrapping elements to hide children elements, whilst preserving the dimensions of the parent element, so as not to break the layout.
I hope that this helps.
That's the answer I was looking for! Thanks a lot for your help!