Mechanical mixers have moving seals that require maintenance and can be a source of entrapment and contamination.
Magnetic mixers only have static seals.

Top mounted mixers don't mix at low levels
Magnetic mixers can mix to the bottom of a vessel.

The long shaft of a top mount can oscillate which can break the mechanical seal or connection.
Magnetic mixers have no shaft or a very short shaft that does not oscillate at the typical mixing speeds.  Also, the mounting post for a magnetic mixer is part of the vessel and provides a solid wall between the inside and outside of the vessel.