An aweful lot of electronics 'beds in' i.e. improves during either the first few weeks or even sometimes over several months does this apply to the pickups do they change over time or are they at their best from day one?
I found that the pickups / magnets stay strong for decades,
but what does 'bed in' - is the way that we ( over time ) experiment with / adjust the pickup heights and types / thicknesses / alloys of string stretched above them e.t.c.
Also a well set up neck / truss rod and a good general set up always seems to help resonance and tone somehow - and
certainly it affects the whole feel of the instrument . And of course when the feel changes, we play / react differently to the guitar as a whole - in a truly 'Holistic' way. I suppose in Piano terms, the way the keys are weighted - and even room humidity can potentially 'change' the way you play and hear the instrument on any given occasion.
So yes, the phenomena of 'bedding in' does occur, but it seems to be one of those enigmas - where the total ( percieved changes ) are greater than the sum of the variables / parts.
Of course with amplifiers ( as has already been observed ) the 'decline' or 'desirable on set of vintage character ' is much more direct due to electrical stresses and heat factors . :)