Magnets are terribly useful, but if you’ve got a really strong one and the head moves over it, it can cause the air-assist fan to slow down and that will cause a print to cancel. The easy solution is to get one-direction magnets (harder), shielded magnets (easier), or put a piece of metal on one side so the magnet doesn’t pull up (magnets pulled from old hard drives already have this!)
You can verify whether your magnets might have this issue by gently waving a metal tool about an inch over them - if the head moves then the magnet can reach the air-assist fan. If the tool is uneffected than your magnets are weak enough there shouldn’t be an issue.
That being said - 99% of the time I use honeycomb hold down pins. I only break out the magnets when I’ve got something particularly wavy.