I notice my yozuri minnow lures and some of my yum money minnow swimbaits are missing there eyes after there being used. Has anyone else seen this too? Are they falling off or are the bass ripping them out during the violent strikes.

Could be a number of things. What you mentioned, banging into hard objects, etc. It shouldn't really make a difference though.

Fish wont care.

I have lures missing half their paint that seem to work better than shiny new ones.

A black sharpie will put eyes back on a bait and they won't fall off then I have lots of baits without eyes, usually as a result of bouncing off rocks or docks. 

With hollowbelly swimbaits, it's bound to happen. The nature of the beast if you will. With hard baits, it annoys me, especially if it happens to more premium lures. Whether or not it makes a difference to the fish I do not know, but from an early age I always heard it preached that eyes are a focal kill point on the lure. Guys used to take sharpies to Wiggle Warts eyes to make them more pronounced, in an effort to draw more strikes. Due to this, whenever I have a hard bait lose an eye, I lose a lot of confidence in the lure. Call it not being able to teach an old dog new tricks, but it just kills my momentum with the bait. I usually change the lure out right there, and then epoxy on a new eye when I get off the lake. 

These lures aren't cheap I hate to see them lose there eyes so easy. But maybe it's the bass ripping them off.

_{Usually, the lures that are missing eyes and paint are the best lures in your box.}

Agree they won't care and also agree use a Sharpie if that makes you feel more confident about the baits.

My main spook bait is a Sammy 115 with one eye, and pretty much worn down to raw plastic.

I have one pointer that's missing both eyes and it seems to produce more bites than one I have of the same color with eyes haha.