I don't know if the MFM does anything to the merchants' damage models but if you also installed GWX3 prior to adding the MFM, GWX *does* makes changes. Primarily in the way merchants take damage, with GWX it's mostly flooding that will cause them to sink, which can take a lot more time and/or holes in a ship (as it does in real life) than what you were used to with the stock game.
If you are pumping 3-4 eels into a small to medium merchant in a very short time using GWX, yes it may sink a lot quicker but it might have sunk anyway with 1-2 hits. It's just a matter of being patient and letting the flooding from the first hit(s) do its job. It is unlikely that a ship of any substantial size will take catastrophic damage and sink immediately from just one hit, unless it's a really well-placed and/or lucky one or some other factors like the weather and sea-state are also working in your favor to cause faster and heavier flooding.
Unless it was a Passenger/Cargo, in which case its holds were full of life preservers and ping pong balls and it's not going to sink even if you cut the bloody thing in half.
