In my experience (having also had thumb discomfort on ergo boards) thumb clusters can be great, but you have to make sure to avoid too much thumb movement.
When I first got a keyboard with a thumb cluster that had 6 keys I was originally a bit overzealous and had a bunch of relatively frequently used keys assigned to them. I actually ended up developing a little bit of what I think was some tendonitis in my thumbs when I first started using it quite a bit.
Ever since then, I primarily only use two of the keys of each thumb clusters with frequency, and they both require very little movement to reach (the two large keys on a kinesis 360). The others that require a little bit more extending of the thumb are more infrequently used keys that don't ring all the time.
In my experience (having also had thumb discomfort on ergo boards) thumb clusters can be great, but you have to make sure to avoid too much thumb movement.