Well, I can tell you that ferrite magnet material is a bit lossier than standard ferrites at RF frequencies, so it should work somewhat better as a choke, if a closed magnetic path is provided. The fact that it is magnetized has essentially no effect on the performance otherwise.
But, if I understand correctly, he has wound multiple turns over a bar magnet. This increases the inductance of the by the square of the turns, but the Q of the inductance actually goes down when you do this, generally making that approach less effective. That's why you don't see multiple turns through standard ferrite cylinders in most cases.
In his case, putting multiple turns through a standard ferrite cyclinder would accomplish a more effective choke, as would adding multiples of the ferrite cyclinders, rather than just 1.
Personally, I would bet hard money he has a wiring issue of some sort -either powered off the same battery as the TM, or routed the wires for the sonar's power or transducer too close, or alongside, the TM wiring. He would be far better off to address those issues, if possible.