Have you tested it on the trailer running with hood off ? Or rode it with the hood off ? I would eliminate leaking water lines as the first possibility... It also probably has a single lip hood seal they don't seal at all especially when old.
If everything is tight I can't see a bad through hull bearing putting 3 inches of water in a x2 in 30 minutes of "ride time" with a working syphon bilge "is it working?" unless the through hull bearing is totally compromised and the seals are totally non existent.
There is 4 seals in the through hull 2 single lip and 2 double lip. And a bearing.