All in all I really like the design of version 2. The idea of having the tags at the bottom is unique and look good. I would also move the WYSIWYG/Markdown switch to the settings menu I dont think people will regular switch between these two modes and it leaves more space for more important information.
I am not sure if I like the position of the search bar, because it implies that only the selected notebook (and potentially sub-notebooks?) will be searched. Is that the case or is it still a general search?
For To-Dos I would actually like it, if the date and time of an alarm is shown below the title in the list. Similar to version 1 but just for alarms not for the creation date.