So many people touch those cards - think about the bar staff. You order from a waiter and they take your card, they have it with the cards of several others, finally going to the bar to get all the drinks, they are scanned for the receipts, then returned, where you use their pen to sign and I don't like to think about what's on those pens.
Speed is the issue with security taking the cards and scanning them. I've had it both ways, with guests putting their cards in the reader, and it is slower because of lack of familiarity, or they put the card in the wrong way, etc. Perhaps if they made the card readers more user friendly, with at least an image showing how to place the card in it.
I tend to notice practices that could spread contamination because I spent my career in radiation protection and radioactive contamination control. It can be a curse if I think about it too much, especially if I'm sitting at a ship's bar and just watch the bartenders hands for 5 minutes when they are busy. Just don't ask for a lime with your beer and please don't nibble on the decorative fruit or give the cherry to your kid.