I very strongly agree with you.
Joseph should be on the birth certificate, and then you can call him
Joey, which will most likely be shortened to
Joe as he grows older. If your son grows up to be a professional,
Joey will seem ridiculous on his business cards. What's the harm in putting
Joseph on his birth certificate? It gives him more options---he can be
Joey or
Joe or
Joseph. I do really dislike nicknames as given names in general, but I dislike the idea of
Joey more than most others, such as
Beth instead of
Elizabeth, because I find
Joey particularly childish.
I have to say, though, I wouldn't use a name I'm not crazy about to get to a nickname I like. I wouldn't put the nickname on the birth certificate either. I'd abandon the idea altogether. But you may be different.