Handicapped or not, NO ONE has the right to try to hurry someone else out of the restroom, period, end of story. Handicapped accessible stalls are NOT for the exclusive use of the handicapped, they are simply ACCESSIBLE to the handicapped. Anyone is permitted to use them, and no one is entitled to an explanation as to why they used them.
And to answer your question, no, I don't let the person inside know that I'm waiting because that would be rude, IMO. Much like a parking space, a bathroom stall, handicapped or not, belongs to the person using it until she is done using it. Two minutes, five minutes, ten minutes or 20 minutes.