Those are patches over holes resulting from excessive buffing, and not very professionally done at that.
To the question of 'What happened to this horn?' I have to say simply 'Everything'. I had one like that I bought new in 1966 and even picked it out at the factory in Elkhart, but I was young and stupid and really didn't take care of it. I also dropped it one night, putting a kink in the body. It has been buffed and lacquered twice that I remember, with resultant tone hole dishing. The body was straightened, the tones holes pulled up and leveled and it even was cryo'd. The neck has one of those patches on it plus another round one on top just past the cork, which was put there for a pickup. The keys have been swedged, the pads replaced many times, a few solders here and there. The engraving is pretty much gone and the owner of it now is using a factory replacement neck on it but the thing is still in service, and he says his repairman thinks he could get $4K for it.
The sax in question looks pretty bad but who's to say what it could bring? Just for parts it would be $2500. If it plays probably $3500.
The neck was probably pulled down. It may have developed a crack in the wall and then patched.
The thumb rest patch looks like it may have occurred due to the player rubbing the area and having an acidic system. Acid probably accounts for the loss of lacquer as well. I've seen that type repair on other horns including a great playing SBA that John Michalak owns.
The neck might have some effect on playing but probably not the thumb rest repair. Hard to tell about the rest of the sax from just the two pictures.
The patches themselves on the neck and near the thumb rest aren't necessarily rare, but at the same time, the horn has obviously been "rode hard and put away wet". I'll also say those pictures prove that some people shouldn't be allowed to do solder jobs to potentially nice horns. Just shoddy work IMO.
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