It seems to me that the Basilisk just didn't leave the pipes, except for its head. Staying inside the pipes, it could avoid everything. It went to find it'sits target, then simply poked it'sits head out, attacked, and went back in. The portraits might have seen something, but it seems to me their gaze would be more along the hallways. It seems like the attacks all happened near Bathrooms, and there was always a puddle of water around. However the Basilisk made the attacks, it didn't wander much outside of the plumbing, and for whatever reason, the pictures didn't see it.