Widening the endpin hole and filling it with a jack will have zero effect on the unplugged sound. Zero. And as others have said, if and when you decide to "permanently" install another pickup, the jack hole will be needed anyway.I'm less concerned about ruining the value of it (by permanently installing one) than I am altering the unplugged sound. If I do something permanent I figured I wouldn't use a soundhole pickup but either an under saddle or internal microphone.
And there's really no such thing as "permanently" installing a pickup, btw. Any system can be removed and the hole filled with an oversized endpin.