As Jack said, the GPS is speed over ground (SOG) including effects of any current that might be there (aiding or hurting) A knotmeter is the better tool for 'boat speed', esp as a result of changes in sailtrim. Having both allows you to quantify the current and approx direction.
You'll get up to 'hull speed' sooner, typically, while beating because your apparent wind is the highest it can be for the wind speed... a clean boat will get there quite easily, as you've observed. Without a lot of breeze or swells truly exceeding hull speed is quite difficult.
Also some boats are said to 'extend' their waterline while sailing (as flat overhanging stern counters become submerged by the rising stern wave) therefore theoretically creating a longer LWL at that moment, perhaps 'skewing' the calculation.
Anyhow, I wouldn't get 'hung up' on the number.. find out what is comfortable for your boat (heel angle and apparent wind angle,)and use that number , whatever it is, as a target and steer for that when trying to optimize your VMG to windward. Polar diagrams may be available for your boat that would tell you what that optimum speed/angle would be. But even with that data you'd need to be certain your instruments are accurate.. not always easy to do.
1984 Fast/Nicholson 345 "FastForward"
".. there is much you could do at sea with common sense.. and very little you could do without it.."
Capt G E Ericson (from "The Cruel Sea" by Nicholas Monsarrat)