Spot on, there are a lot of people who lurk around the internet in weird ways and sometimes won't be counted by various things. GA will definitely miss these people.
There's also the tin-foil hat crew who would tell you GA intentionally mis counts in an attempt to disrupt their attempts to manipulate Google's algo.
CPanel counts everything and I tend not pay attention to it. If you're looking at the number between GA and WP, you'll have a pretty accurate picture. WP will be way more helpful to see how people find you through search as it will report key words from those logged into their google account; GA will not.
GA will be way more helpful in reporting non search traffic, WP tends to suck at this.
