We do kinda know the answer to that actually. This is something that was done prior to the Yamaha takeover, so I do not know what Yamaha's plans are, but, generally speaking...during covid and it's domino effect/simultaneous catastrophies, there were major supply chain issues, some of which continue to this day, and all of which resulted in significant price increases across the spectrum (at least as how they relate to guitars).
So the first problem was that there was a legit shortage of pickups for the acoustics, likely made worse by Guild being essentially at the bottom of any priorty list, of anyone needing a large volume of said pickups. They could not get enough pickups for all of thier A/E units of all models, and certainly they could not get all the same pickup manufacturer nor the same model pickup within each manufacturer. So on a mass scale, they could not advertise that you would be getting a specific make and model pickup in any given guitar, and possibly they would have no pickup at all whatsoever, for you, for any Guild guitar at all, at any given moment. So the choice was chaos within all acoustic Guild models that electronics were offered on, or simply remove that option for the entire line of D-20's...and then for the D-40's as well.
My belief is that a second reason this happened, is the price of those pickups went up a lot, and it costs Guild additional then to install them, and to a degree warrantee that work as well (and possibly warrantee the pickups, or at least have to deal with it thru baggs or fisheman, etc). I think they were always trying to keep the D-20 as affordable as possible, and possibly the D-40 as well (at least compared to D-55 or F-512). With the mentality that the end user can obtain thier own pickup of choice, at the price they want to pay, install it on thier own, and pass along all of those expenses and liabilities to the customer...it just evolved to the point where the customer was going to get the guitar for a *lot less money than Guild would be able to sell it to them if it had electronics. It makes a much bigger difference on a $1,200 guitar than it does on a $4,500 guitar, if you follow all that.