What kind of bug is doing these holes

A bed frame is at best going to support the box-spring around the edges (perhaps even somewhere in the middle if there is an extra cross member).

If the box spring is on the floor (or a platform bed), then it's supported everywhere. Which in my opinion is better for the mattress. Of course, your wife may dislike the look of it on the floor.

I'd chock it up to either having a very fun 3 years, or poor quality mattress.

Wood isn't going to harbor bedbugs. Upholstery might, but if this is your trigger I would bet dollars to donuts that this is simply autosuggestion.

When I was a kid, I had my brother conditioned to the point where I just said "ants" and he'd start to itch, whether ants were possible or not... It really isn't hard to convince yourself that you might feel something when nothing is there, or to convince others by suggesting the idea to them... even unintentionally by scratching more than usual.

(My most successful bit of suggestion was many years later, as a college student. I'd learned a bit about self-hypnosis, and I'd learned that under some circumstances I could distort my vision by deliberately misinterpreting perspective. When I was particularly bored, I would sometimes "levitate" an object by momentarily convincing myself that it was a bit closer to me than it actually was, and therefore had to be floating over the floor or table rather than sitting on it. One day some friends and I were in a restaurant, waiting for our order, and I started playing with this... and one of them noticed me staring fixedly at the salt shaker, with my body language suggesting that I was pulling upward on it, and for a moment got caught in the illusion. Shocked the heck out of him...)