DC motor with two magnets (exactly describing my motor) would act as a compass. Not sure what I could do to compensate.
I thought to it in these days. One possibility could be to make the flywheel to spin by inertia, without motor.
So there would be no problems related to the magnets.
There should be no need for a very long spin duration, after all; even after just 1 minute spinning, Earth rotated by 0.25 degrees, which is an angle easy to detect, using a laser pen and a mirror on the small floating boat, like in the YouTube videos we saw.
The problem of not having a motor is that the deceleration of the flywheel would cause a torque on the small boat;
if the plane of the flywheel is set at 43 degrees, a component of this torque would make the boat to rotate on the water and the stable orientation would be rapidly lost.
This problem can be overcome by setting the rotation axis of the flywheel exactly horizontal;
in this way, the torque from the decelerating flywheel would have no effect on the orientation of the small boat, which would remain stable.
The construction would be not too complicated, because it's a flywheel with two bearings, mounted on the small boat, no gimbals needed.
The horizontality of the rotation axis of the flywheel can be fine tuned by moving some weight in the boat from stern to bow or from bow to stern.
I believe in fact that it is not necessary the plane of the flywheel to be set at 43 degrees.
The Foucault pendulum works even at the intermediate latitudes, even if its plane of oscillation is always vertical; in the same way, the spinning flywheel should be able to follow the rotation of Earth, at the intermediate latitudes, even if the plane of its flywheel is vertical.
As for the problem of the currents, maybe it could be better to use oil instead of water;
water evaporates and this makes its surface to be colder, this certainly causes some currents in the water, with the colder water moving downwards.
The currents can move the small boat and hamper its stable orientation.
We want the liquid to be as steady as possible, so it could be better to use a liquid which does not evaporate, and that has the same temperature of the surrounding environment; also, with a sufficiently steady liquid, it would be not necessary anymore to use a device to maintain the small boat at the center of the pool.