It depends on the motherboard itself.
You *should* have a screw/standoff for each mounting hole on the motherboard itself, that way it doesn't get warped from being hot and cold, causing problems with the circuitry.
If there is one or two standoff holes on the motherboard that the case doesn't have then it should be too big of an issue, depending on where the holes are at. If you have missing standoffs near the CPU then that is prolly not a good deal. But if one missing on a corner or empty area then not so bad.
Also, if you are talking about a punched/raised metal part of the case plate in some mounting positions, and no raised metal, but just a screw hole in other positions, then you need the little plastic standoffs for the screw hole(not the raised metal), and you should just use a screw on the raised metal on the plate.
Raised metal only(looks like a hump on the plate) = just a screw to the motherboard
Drilled hole only(metal is flat) = plastic standoff + screw to the motherboard.