With Notepad++ 5.9.3 Unicode on Windows XP SP3 and Window Manager plugin v1.2.2, I have found the plugin slows down greatly Notepad++ when there are many files open (250). And in my case, most of these files are on a network share. Also note that I configured WindowManager to display the files sorted by name.
To open Notepad++ for the first time when the WindowManager is hidden, it takes about 30 sec. When the WindowManager is displayed (because it was displayed when NP++ was last closed), it takes about 4-5 minutes. Similar differences for closing Notepad++ application. However, the presence of WindowManager does not change the time to get the focus on NP++.
I guess WindowManager sorts and updates the files each time one is loaded/closed by NP++ while NP++ opens/closes. Could WindowManager ignore open/close messages sent by NP++ to the plugin while NP++ opens/closes? When NP++ has finished opening the last file, then WindowManager could update the file list. Once and for all.
Another solution would be to optimize the WindowManager file list refresh algorithm.
When I close my computer each evening, I have to think closing NP++ first because I know I'll still wait after it after having closed all my other applications. With the workaround of masking WindowManager, it is better. But a solution should be implemented to avoid having to do that workaround.