I think I figured it out. The original reflects a view that actually exists. The 1940 uses a manipulated view.
The Charles bridge has a number of pillars, with arches in-between. On each of the pillars, on both sides of the bridge is a more or less religious statue, so that there are two rows of statues, all looking away from the water and onto the row of statues on the other side. The coins show only three of the arches from the water (the backs of the statues are towards the engraver).
I used Google maps to make the pictures. I could deduce which statues are on the original, because a) their silhouet by and large matches the ones on the coin and b) they are directly opposite the statues on the 1940 issues. I have not identified the group at the centre (image: old centre). On the left is St. Christopher, carrying Christ across the river (old left).
The 1940 issue uses the statues directly opposite (new centre and new left). The group in the centre is St. François Xavier. I could not identify the statue on the left. Both have an outstretched arm that points in the very general direction of the castle. On the picture "new left" you see a church sticking out above the roofs. It is actually on the grounds of the castle. Keep in mind that this picture was taken from the bridge, face towards the camera.
I think the view on the 1940 issue is across the bridge, deleting the railing and the statues shown in the old version. If the view would have been from the other side of the bridge, the left statue would have appeared on the right. However, I may have identified the statues wrongly.
Peter