Fortunately, I don't work for a manager who would send me just a "?", but if I did, it would go ignored. I think it would tickle me if they followed up with "?!".
Yep. It's become more of a "hey you, look at me" kind of thing for us with my '?' being a "yo, you've got my attention- what's up?" kind of response. It works this way for him and I, but I wouldn't expect it to be an inherent shorthand in any of my other relationships.