Why do my Android text messages (SMS) take minutes to send?
The HTC Mail and Messaging apps may have memory leak issues -- if this is the case, having a large DB of messages could cause a slowdown.

I had some system slowdowns and freezes. After I started using the K9Mail/Gmail and Handcent SMS apps -- I had no more slowdowns or freezes.

Since HTC apps cannot be uninstalled or turned off (unless you root), you can only set them to never poll for messages and never alert upon receipt of message. Which it shouldn't get. But you never know.