You can add/change the motherboard mounting screws (risers) underneath it... but to answer your question, it's not important that every single hole have a screw. As long as you have 4 or so, you'll be fine
If you have fewer number of screws attached, you might break the motherboard when you try to install an add-on card. If the add-on card (such as a gfx card, PCIe card, RAM modules, etc.) is difficult to install and you have to press it forcefully to seat it, the motherboard may break because it will not have the proper reinforcement underneath. Of course, it all depends on where the screws are missing.
If you can remove any of the motherboard mounting screw risers that do not line up, otherwise if they contact the motherboard, they can produce a short circuit damaging the mother board and/or power supply.