Usually there are 8 or 10 or 12 total standoffs, IOW quite a few. Missing one or several normally won't make much difference. In an extreme case your motherboard could be bending due to the weight of the cpu cooler. You have to make sure that isn't happening, and make sure the back of the motherboard isn't touching anything inside of the case that it shouldn't be touching, like the missing standoff.
If you need standoffs, any normal computer store should be able to give you a few. Or you might move around the ones you have. Some places on the motherboard are just sitting there without any load on them and don't really require connection to the case.