If the aqueduct held 1000 tons of water, and you put a 10 ton boat in it, it now contains 990 tons of water and ten tons of boat.
No (but I know why you are proposing this, because you're not precisely defining the extents of the system).
The system as a whole now weighs 1010 tons. You don't magically cause 10 tons of water to disappear from the system by dropping a 10 ton boat into it (unless the water level is at the brim somewhere and dropping your boat in causes it to overflow)
Do the aqueduct supports feel the weight of the barge?
They already feel the weight of the barge, and have done in whatever proportion of the surface area of the system the aqueduct represents ever since the barge was added to the canal.
An aqueduct is 100m long. It is the only thing in the canal system. Nothing else has been built yet. No barges are in the system. It is essentially a large bathtub on stilts and carries 1000 tons of water. A ten ton barge is added to the system. The supports must now carry 1010 tons. The supports feel the weight of the barge
The barge is taken out and the canal system has some more work done on it. 50m of ground either side of the aqueduct is trenched out, same width as the aqueduct. The system is topped up with water and now contains 2000 tons of water and as a whole is 200m long, twice what it was before. A 10 ton barge is added to the system. The system as a whole now weighs 2010 tons. The aqueduct supports experience half of the weight of the barge. The other half is borne by the ground that was trenched out either side; the weight of the barge is spread
To the question of moving the barge around and whether this causes a change in the weight the supports experience, it does rather depend how infinitesimally persnickety you want to be with regards to the answer. Let's be extreme, and turn our barge sideways then drag it by both ends, establishing a large bow wave such that there is barely any water at all behind the barge and it's all piling up in front of it, and the aqueduct sides are tall enough to contain the wave. As the barge passes over the aqueduct, pushing this massive wave of water with it, the aqueduct will experience the extra weight of the wave, as it's effectively a temporary return to something like what we had before (the system closed at both ends, causing all the water to sit on the aqueduct). This time it isn't closed at both ends so there isn't a large volume of water sitting static above the bridge, but the fact that end is moving and pushing the water with it means that for a short time, we're piling water up over the bridge.
If it's hard to conceive, let's have two barges that are a really good fit when wedged sideways in the canal, barely any water gets past them. Let's drag them towards each other so the water level builds up between them, until it can't escape past them he sides and under and establish a level. For the time that extra water over and above the resting canal level, is piled up on top of the bridge its weight has to be borne by the bridge
Your question is too loosely stated to be able to answer effectively but if you're willing to accept any change in weight, however small, then yes the stanchions of the aqueduct will experience some change in the amount of weight they have to bear if anything moves in the water such that it pushes some water from somewhere "not above the bridge" to become "above the bridge". A duck swimming onto the bridge, pushing a a small wave ahead of itself that ripples across the water on the bridge as it peters out will temporarily cause a few extra grams to be borne by the bridge
Does taking some minutes to sail a 10 ton barge over an aqueduct carrying 1000tons of water, cause the supports to have to carry an extra 10 tons for some minutes? No
Does taking some minutes to drag a vastly hydro-undynamic object through the water such that 10 tons of water ends up piled up in front of the object, proceeding along at the same speed as that object (as the object chases the wave down the canal), cause the supports to have to bear an extra 10 tons for those minutes? Yes