Traditionally speaking, whomever the invite is specifically addressed to is/are the one/s invited. So you can write whatever you want on the standard invite, but if you address it to "Mr and Mrs Joe Smith" they are both invited.
I think about 50% of common day society would understand this.
I'd consider switching the title to "co-ed shower" or "co-ed Baby-Q" or "a co-ed celebration in honor of the upcoming arrival of baby X". I believe that for most people, the words "baby shower" would imply a females only celebration.
All of this. Addressing the invite to Mr. and Mrs. Joe Smith should let people know that it is a co-ed shower. However, for the people that don't pay attention to the envelope, having the phrase "co-ed shower" on the invite should make it clear.