Hall effect sensor expert here! No, the magnets in the joycons that are used to attach to the display/body of the Switch 2 would not interfere with hall effect analog sticks.

Two reasons:

• The magnets are too far away (sensors are usually only sensitive within 10-12mm directly above/below)
• The mounting/attachment magnets would be perpendicular to the magnets in the analog sticks (if you imagine the flux lines they wouldn’t cross the sensory boundary).

Regardless, it would be trivial to place a tiny little piece of ferromagnetic blocking tape wherever necessary to prevent interference.