Well the biggest downside to cpanel is it loves to eat memory. It runs a few different monitoring programs and things that will suck your memory dry. You can disable a lot of these, and it should help your performance. Making sure its configured for best performance should help a lot but if your still having trouble with it being laggy upgrading the CPU may help. PHP scripts use a lot of CPU power to run.
Perhaps a Core2Quad Q6600 2.4GHz with 4GB ram would help, cost ya about 230/month including cpanel and everything.
No the pages do not go "through" cpanel. Its just the programs I mentioned above that it runs in the background that chips away at your ram and even cpu at times.
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