|The problem with a missing standoff is that inserting expansion cards or RAM can flex the board and possibly cause damage.|
I take it you don't have any spare standoffs and screws? Keep in mind there are different length standoffs too. Most are the same but there are some cases that for whatever reason use shorter ones. Nylon spacers will work too, if you have them.
The purpose of the standoffs is to keep the board from shorting out on the case. Flexing when inserting stuff is what you need to be concerned with. If you can deal with that then you should be OK with one missing. If you are not using any expansion PCI cards you could leave out one at the bottom.