Reed says that the EPS conduits are too tight for Trip or himself to fit. Only Hoshi is small enough, but when we see her in the conduits she has at least 6 inches on each side. Reed and Trip are not that much bigger than Hoshi.
When Hoshi gets the hypo-sprays from the doctor she speaks rather loudly. Her voice would be carried by the air ducts efficiently, possibly all over the deck. Add to that the Suliban's enhanced hearing and the possibility of her being discovered is quite high.
It is not clear why Hoshi is not wearing undergarments under her shirt when it comes off, although it is likely due to the show's change to put forth a more sexual side.