Kopete _must_ be compiled with aRts for the flashing event to work in the taskbar. My personnal opinion is that this is a bug. KDE devs will most probably not see it as so, even though KDE 4.0 gets rid of aRts. (Probably has to do with having all events treated as same and makes their code cleaner, less #ifdefs all over the place).
Anyways, people should definately know or be warned about this.
It's a known issue that kde requires arts for notifications also if arts is not used at all with them (example you use an external application to play sounds or you have only visual notifications).
There are already bugs opened upstream, please refer to them to see the reasons why it's not easy to remove arts from 3.x series.