It depends on what you mean by "something happens". As seoulja said, if that something is the drive dying, C and E are gone. Because those are the drives on that drive. If that something is C gets corrupted somehow then E is fine. You can format C only and all the data on E is safe. You said however E is empty so there is no data there.
Some people like single drives/partitions. Others are like me and partition everything. (No joke, I'm up to drive U on my PC.) As long as C has enough space for windows and everything then you are fine to leave E alone. It's totally up to you and how you do things.