Well, we do have a mystery here or what?
I would have agreed with Garry that the two seals on the bottom should do the trick, particularly if they are pressed against the flat fiberglass surface of the boat. However my experience tells me otherwise and I have had water coming in two out of the three years I have owned my SM2000 in spite of 3 full seal changes.
The first leak happened on the inaugural trip from Fort Pierce to Savanna. The previous owner had just changed all the 3 seals weeks before the sale. During the overnight passage we had no particularly large waves under a nice 15 knots reach. However, after I arrived to Savanna, I found the forward bilge had salt water almost up to the floor! Not the kind of thing a new boat owner wants to see after his first cruise. In the slip, I make sure the water was not coming from anywhere else, and that the boat was not sinking. Then, I changed the 3 foam and the lip seals and reduced by a half turn the length of the shaft to increase the compression to the bottom seals when the pin is in. Results: no more water for two seasons.

Last spring I first noted a small leak that increased progressively and, by the middle of the season, I was getting two good gallons of water in a trip from Boston to Province Town. After I saw with my own eyes that the water coming through between the lip seal and the shaft, I made an extra seal that I could wrap around the shaft, which kept the leak at bait for the rest of the season. I will be posting pictures of the seal because I think something like this should be on every Amel spare part box.
Any way today, with the boat on the ground, I took the thruster out and found that the (lip) seal around the shaft was, as expected, stretched. However, both the bottom and the top foam seals were absolutely intact. So Garry, this trashes the theory that the bottom foam seals, compressed with enough pressure, can prevent the water from coming in. Remember that I removed a turn increasing considerably the compression on the foam seals with the pin in.
Question for the forum: how can water get around the two bottom foam seals under good compression? The sealing surface from below looks nice and flat. For me this is a mystery.