1988 Toyota 4Runner Now they say its the clutch

I heard lots of noises under the car and took it to my repair shop I've been going to for the past 24 years and they said the noise was due to some loose "bearings" and that it would cost about $450 to repair. After a while, I went ahead and got it done, but almost as soon as I drove it off the lot I heard the noise again and called the shop. I made an appointment to come back in, but never got around to it until now.
Yesterday as I was pulling out of a parking lot and after driving about 1 mile I noticed the clutch was sticking. I've encountered having to pull my floor pad away from the clutch on occasion to make the car start, but this one was different. This time the I could not put the car in gear and the clutch went all the way down to the floor.
I had to have the car towed to my repair shop and was angered that they could not tell that it was possibly my clutch that was making that original noise, and now they want to charge me another $450 to replace the clutch when all they did before was tighten up some bearings.
Is it possible they could have seen that my clutch was wearing out or was the original cause of the noise? They still seem to think my clutch had nothing to do with the noise. Its a very loud "clunk". Are they right? Could the noise have nothing to do with my clutch going out?