The bacteria are in an environment very different than the human body. So while there may be a lot of bacteria, it's probably not going to do any harm to you because it's not adapted to infect you.

Speaking as someone who has done a decent amount of caving, I'd be much more worried about the CO2 and other gasses in the air (and I'm sure those scientists are as well). It's really rare for caves to have dangerous bad air. But sounds like this one could be an exception.

Water currents enter and exit from caves. Aquatic fauna do the same and Nepa can fly easily or enter in crevices if it senses water. That said, the species shown are strange for Europe. I wouldn't discard that there are some misplaced photos (or the authors toke some literary licenses).