I was perusing my '00 RM250 service manual this weekend, and it calls it something like an airbox-top-cover. They say to leave it on, or it may alter your jetting. (that can be taken for what it's worth, being written from the manufacturers standpoint.)
I do leave mine in place - my bike is a bit louder without it, and I like that it keeps mud or junk from falling directly onto the filter.