I don't really see how hiding an upgrade could work. Yes it would work wonders in a private 1 on 1 game. However in a tournament, early finishers will be able to see what you've hidden if they observe you and negate any surprise hiding the card could be. Plus what upgrade you do have could give away the type of upgrade you are hiding, which for something like a canon, really limits what it could be down to HLC, Ion Canon and Autoblaster...three choices which the opponent could anticipate.
Edit: I don't mean to sound to harsh! It's a lovely idea...but I can't see people using it much.
Oh yeah; as far as competitive games go, I totally agree - this would amount to a waste of points. But I think it would be fun, and pretty useful in casual games. The difference between a Proton Torpedo and an Advanced Proton Torpedo, or an Ion Torpedo for example, is pretty significant. It's a good way to play mind games with your opponent, I think.. but yeah - only really useful for casual play.