http://forums.microsoft.com/TechNet/ShowPost.aspx?PostID=1203630&SiteID=17
I'd recommend first to investigate the performance problems and find the cause. The BOL has a troubleshooting guide that is very useful at isolating out the problem: http://www.microsoft.com/technet/prodtechnol/sql/2005/tsprfprb.mspx
Once we know what the problem is, we can answer wether Query Notifications is at fault and if there is something you can tune about it.