Probably this is a giant feature which would require an insane rewrite/big addition of code/whatever so perhaps it will never happen, but, for the sake of getting the suggestion on the table:
My ideal version of Hypernomicon would be one which optionally allows for multiple windows. So for instance if I could drag the "Tree" tab out of the main window into its own window and put it on a separate monitor, then drag a Term from the Tree into the Work to embed the Term, that would be neat. If I could right click on a Work and choose "Open in new window" and then alt-tab between that Work and another Work at the same time, that would be neat. If I could have two Arguments (one for X and one against X) open in separate windows and tab between them to edit them both (because I'm reading a survey article which is summarizing the "for" and "against" positions) that would be neat. Etc.
I agree with pretty much all of this (and I also suspect it's a huge job!)