I've never seen a ski break at the holes, but in the bigger picture, extra holes in the ski are a weak point, and do allow more potential for water ingress.
And most importantly, the number of mounts a ski has is a huge factor in how much you can resell them for. When I'm selling or buying skis I calculate each mount to be about $150 of the value of the ski, all other things being equal. More holes just means swapping bindings is gonna be more of a pain in the ass.
Ski shops NEED to replace skis they fuck up the mount on. It happens way too much, and because there's not enough of a penalty for it, it keeps happening. It's absolutely nuts that a shop can get away with effectively ruining a brand new pair of $800 skis and offer you a free tune that costs them like $20 in time and materials. In what other industry are you allowed to freaking drill holes in a brand new product, altering it permanently, and then have barely any consequence for your actions. If this happened to mountain bikers they'd be up in arms, but for some reason ski shops still get away with it.