Not sure who you are. Sign of with name, name of boat, and type and hull number e.g.SN 01.
The seals are neoprene. I guess as a temporary measure you could cut them out of neoprene or an old wetsuit! There should be just one inside the boat visible where the shaft goes through the whole. If, as you say, there are two, then it is most likely that there is only one underneath, where there should be two. The previous owner may have installed them the wrong way round. This would also be a likely cause of water coming in.
I guess you might have looked up on the AMEL owner’s web site how to service the bow thruster and replace the seals. It is the same as the Super Maramu.
A couple of suggestions.
Take the pin out. Squeeze the cable as tight as you can and see how far the pin hole rises above where it should be. If it goes a long way (which it could if there is only one neoprene seal on the underside) then the clearly it cannot keep the water out. A temporary improvement can be made by tightening up the threaded nut at the top.
There is a post on how to do this adjustment on the AMEL site with photos. If you search Ocean Hobo bow thruster you should get there.
I don’t have the AMEL tool for lowering the bow thruster. It does do this job, but I also think it has to plug the top of the tube as this is where the oil reservoir is. You don’t want salt water getting in there!
I too have fitted a bilge pump next to my speed transducer in the forward toilet corridor. I fitted a small bore outlet pipe into the shower tray below the wooden grating. I get rain water in there too from the anchor chain hawse hole.
Good luck - it takes a couple of years to get to know all the systems on your Santorin. It is a great boat.
Ocean Hobo. SN96 currently locked down in Wales.