No. This is easily the weakest part of Smalltalk IDEs. And with Morphic-based ones, you can't even fix it with a tiling window manager or something, since it's just one window for the rest of the OS. There's no way of organizing the windows in groups, no automatic placement, no virtual desktops. The best you can do is simply get into a habit of culling unnecessary windows. It's emotionally hard to close windows you spent 10 minutes searching in for the code you might (or might not) need in the future, so I made a simple sidebar[1] that I use to bookmark useful stuff. With it, I can close windows with impunity.

[1] https://klibert.pl/statics/smalltalk/sidebar.png