Sam is correct. This is not a WinUAE issue, it is an OCS/ECS quirk. If you need a hires pointer you'll need to roll your own using a BOB. Hide the mouse pointer and each frame read the mouse x and y coords before resetting the mouse position to the center of the screen. Subtract the x and y coordinate of the center of the screen from the x and y coords returned by the mouse functions and you'll get the change in x and y: dx,dy.
You can then move the BOB image "pointer" by dx,dy. This will move the pointer in sync with the mouse, and since the BOB image is the same resolution as the screen it will be hires.
One drawback though is that mouse movement will be half speed in the naive implementation of this. You could do your own mouse acceleration routine, say if dx is less than 10 pixels, use the above routine so exact pixel position is maintained, but if dx > 10 then dx = dx * 2 or some other factor. Do the same for dy.