we should not be able to measure thrust because, in space all motion is relative.
How exactly does that affect measurement of thrust?
Taking thrust to be the forward force behind acceleration, can be found easily enough. For example using chemical rockets we know the mass of the propellent and can likely figure out the speed it exits the engine and we also know how long it takes for the fuel to leave the engine. So lets say the fuel starts at 0 ms^-1 and is accelerated to say 30,000ms^-1, mass of fuel is 5kg. Takes 12 seconds to burn. Force = (change in momentum)/time so we can find out that.
But newtons third law kicks in. The force object A impresses of b is equal to the force object b impresses on A. Ie each action has an equal and opposite reaction. We probably know the mass of our own ship and in pushing all those burnt up chemicals out we get forward thrust. Which I've shown in paragraph A can be calculated.
Now I just think you've confused yourself. In space all motion is relative true, but that means we cannot measure our velocity. (How fast are we in relation to what?) not thrust (which leads to acceleration which we can measure).
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To be clear I'm not suggesting speed be hidden because that'd be a huge pain, like really.