A link always opens in the currently active pane (the one you last focused or clicked on) So you can click on a link in the current pane and open a new pane, but you can’t open it in a different currently open pane.
Yes, that’s a problem, but is it the one you are describing?
Related is what happens with the forward and back navigation arrows when you are working with multiple panes. Back returns to the previous note whichever pane it was in, which is confusing. The panes should have independent histories, just as browser tabs have. But in your scheme would each tab also have its own history?
As I understand it, you want control-click to open a new tab in the current pane, which doesn’t solve the problem I started with. Or when a pane has multiple tabs and you then split it, do both panes then have the same tabs, and loading another note in one without doing control-click will reduce it to a single tab?