Well, eggs CAN absorb bacteria, yes. That's why you should wash your hands thoroughly before handling or candling your hatching eggs. But if you've got healthy embryos that have made it as far as day 23 (which is the earliest I would float a late egg) in all probability they aren't going to be affected by bacterial contamination at that late stage. If you use a clean pan, and warm water straight out of your tap (boiled and cooled if you know your tap water isn't good for drinking), and float the egg for just one minute, it won't absorb any water through the shell in that quick time. 
I know some people really don't like the float test, but I've used it loads of times and find it very helpful and in no way detrimental to the chicks. I've also read some reports on BYC of chicks that ended up drowned in the shells after being float tested, but thinking about how quickly water is absorbed by the egg through the shell and being logical about it, I'd bet just about anything that those chicks would have drowned even without being float tested, due to being over-humidified right through the incubation...