KNP,
While I appreciate everyone's comments on "stuff to check", in my opinion performance issues can arise from all manner of configuration settings (issues) as well as (hardware) bottlenecks both on the SMP as well as SQL server predominantly.
Adding the additional endpoints may very well have tipped the scale - or just exposed a configuration issue, say based on new sites not handled by existing site assignments.
In general when the Console slows down - I would look at a couple of things;
1.) SQL/CMDB; What's the fragmentation of the various tables? And do you have a maintenance plan in place.
2.) Parse the IIS logs (if you know how to) and see what page hits are taking place. You may not really have a good baseline, but if you see a lot of task server registrations that would be bad (within short time intervals)
3.) Review the NSE queues (as suggested) as well as reoccuring policies and/or tasks, that might create data. While this may (or may not) show up as CPU utilization it very much will show up as disk I/O on both the SMP and SQL server, so running perfmon on the two might also give you an idea of whether you happened to hit some issue like that.
Last but not least, what is/was your hardware spec'ed out to support, when you add more endpoints your hardware demands are increased, so compare against the installation guide for that too.
For some reference material check out http://www.symantec.com/docs/HOWTO10330 in the Performance Tuning section.
Regards,
Rasmus