Hello,
I can confirm the fact that once you reach around 450+ plugins after a scan then plugins start disappearing from the menu, in a rather random fashion.
I use the standard background scan all plugins view, no crashes or error messages appear ... only the plugins disappearing.
I upgraded from Music Creator 6 to X3.
In music creator 6 you got a message when to much items where in the plugin view, then you could create a number of custom views and actually access & use the plugins.
Now when you create the custom views the plugins are accessible from the custom views, but the ones that 'disappear' from the all plugins views, do not work anymore.
I spent hours trying to figure it out, but I think this might be a software bug.