And there's my answer to another question on the forum re: Hendrix Grip ... thanks DM!
Personally... I have double jointed thumbs... but to the point that they are WEAK double joints (go figure, the thumb on my fretting hand is worse than the one on my strumming hand). I played the clarinet for a few years as a child and gave it up because the weight of the clarinet resting on my thumb (again, my "bad" thumb) was painful as my thumb would slip out of joint while the clarinet was resting on it. Ouch.
I find that my Classical style guitar fits well in my hands and if I try to place my thumb where it "should" be... it pops out and is very uncomfortable causing pain if I push it too much. Conversely, the neck on my husband's electric is too thin and it doesn't seem to matter how I hold on to it or where I put my thumb, it just hurts (of course, this could have to do with the weight of it too?). I assume everyone is different with how/where they can hold the guitar to ease the strain placed on their hands. I also have the beginnings of carpel tunnel and was concerned... but guitar playing doesn't affect me at all (knock on wood)... where typing really does a number on me if I do too much.
sooooo.... try holding on to the neck differently... try it "wrong" ... try that Hendrix grip... and try taking a break with some "easier" chords when it starts to hurt! Maybe take a trip to the guitar store and try out a few different neck styles and see if there's one that fits in your hands better... you've been at it for over a year, maybe it's time for a New Guitar Day!
Art and beauty are in the eyes of the beholder.
What constitutes excellent music is in the ears of the listener.