How does the ports on the board line up with the io shield with out the standoffs? I would think you would be like 1/8 - 1/4 of an inch off. Would make it hard to plug stuff in.
If it was my computer i would install the standoffs correctly. Take the time to blow all the dust and stuff out too.
Theres a little play in the case. Cases are standard, but not *that* standard that it has to be down the millimeter.
It would be a good idea to go back and install the standoffs, however, if the system has run fine for some time, I wouldn't see any cause for immediate harm.
In theory the standoffs aid in getting a clean ground to the chassis, however, some people have custom design open benches and cases utilizing plastic and wood all the time without problem, of course, they generally use standoffs lol.