Indeed, magnets age. They get weaker over time, abd this must affect the output. For a start, it must decrease a bit. If you then adjust the pickup closer to get more output, it will likely change the tone.
Or if you were able to compare the sound, unadjusted and years apart, the magnets would account for most if not all of the change. Movement and drying of wood, particularly if the finish is largely gone a la Rory Gallagher, might also change things a little. But I can't imagine it having a great effect.