Hissing might be hard to distinguish unless it's very clear, in a very quiet environment. A snake that is visible and hissing in a quiet area is much more obvious than a hissing or shushing sound with no visible source.
In a busy castle, the hissing would be muted by the thickness and layering of the walls and pipes, and might also be covered by the noise of people moving about, voices, footsteps, and the occasional bit of drama, like a spell, or shouting, or thumps and bangs. The hissing itself, since it had no visible source, might have been taken for the kind of shushing sound from the movement of water in the pipes, the swishing of fabric (from robes or tapestries), or the distant sweep of the wind.
And people aren't used to listening for hissing - it might not stand out. @Lily K Tudor is right that in that scene they were actively looking for voices, and discounting any other sounds as distractions. As for other places and other times, people might be distracted with their thoughts or each other, they might have clearly heard the hissing but not connected it to a snake or what was going on with the petrificaitons, nor mentioned it so that someone might have a chance of realizing this was happening quite frequently.
Honestly, the basilisk might have been talking to itself daily, and it's likely people wouldn't connect the sound with anything unusual. Maybe Filch had a list of requests "to have someone look at the plumbing, it was sounding kind of loud", that he merely didn't get a chance to before the basilisk was revealed.