Another question would be is there a CPU hog running? Check this by opening Task Manager and checking the CPU rate. The rate of use will vary from moment to moment but generally it should run pretty low, like 5% or 25%. If it consistently runs very high, like 75% or 90% then that will slow everything down, even the movement of that arrow. If you find high CPU use you can get more details by installing Process Explorer or PerfMon. All are good, but Process Explorer also shows DPC's and hardware interrupts...
OK, since CPU use is normal and you have a lot of icons...
Seems like there should be a way of getting rid of icons rather than just hiding them. Most of mine are called "Past Items" in the Customize button of Notification Area of taskbar properties (right click taskbar>Properties). I think I just closed all those programs. Only icons of active programs appear or are hidden. Do the icons in your notification area represent programs that you are using? There are a few ways to stop them from opening if you aren't using them...
How many icons do you have there? – Matthew Steeples – 2011-10-12T17:48:05.453
Twenty two icons? Asking 22 programs to draw their icon indeed takes more than 2 seconds... – Tamara Wijsman – 2011-10-12T21:39:49.613
@Unsigned: I'm not entirely sure, but there is probably something memory related involved like deallocating the memory or paging it to disk. It might even enumerate all the program to tell them that the icon isn't shown anymore to the user, to be sure you would have to look into the Windows API and Windows Internals. But one thing is sure, it does something that is costly on both show/hide... – Tamara Wijsman – 2011-10-13T15:43:20.887