There are knots and there are knots. As a general matter, I suspect it would be unusual for a maker to intentionally choose a terribly knotty slab for a top. A straight, even grain is just one factor contributing to a solid, resonant box. Knots generally weaken wood. I would imagine that an unblemished straight-grained top would vibrate in a "purer" fashion than one with a large knot. Also would likely be relevant where on the top the knots occurred. I would imagine that out towards the corner blocks, near the top block, or outside the f-holes (where I believe the top is the thickest) any weakness/variability would have less effect on the top's vibration than, say, right over the soundpost. But I am the furthest thing from an expert.
It is not unusual for a blemish to appear as a top is being carved. The maker will decide whether or not it interferes with the plate's tone. My wife has one such fiddle. We call it scarface. It sounds great, and we like the look of it, but she has never been able to sell it. Not all buyers appreciate an unconventional look.
Coincidentally, I get emails from Upton, and today's mentioned a new build of theirs that features a knot.