The only thru-hulls that should have a forward facing scoop on a sail boat is the intakes for the for HVAC or refrigeration, they assist in the pumps keeping their prime.
The yard that fitted your thru-hull for the engine raw water intake is incompetent, it is a rookie mistake and even if a rookie installed it there should have been a final inspection before launching by an experienced person. The Yard should haul and correct the problem without you incurring any costs!
Mainesail is correct, raw water pumps do not block the flow, there are wear items in a pump, the 'cam' and the 'cover plate', even a new impeller will not seal properly if these are worn, add a worn impeller to the mix......
It does not take much wave action or to force water into a forward facing thru-hull, particularly when the boat is heeling and the thru-hull is closer to the water-line and the relative height of the thru-hull and the engine is reduced due to the hulls lateral rotation as it heels.
If you cannot get satisfaction with the yard, until you get this corrected, I would not sail the boat without the thru-hull being closed to prevent the possibility engine damage..