I'm a programmer, but in general I find the following two things are generally true:
1. Numbers and symbols aren't a large part of "regular" text.
2. When programming you don't need super fast access to symbols.
So because of that I'm mostly just interested in being able to type regular text quickly for emails, documentation and instant messaging.
I have a kinesis, ergodox and truly ergonomic which all have multiple thumb keys. However I don't find it important to include thumb keys in the layout analyzer as I consider a thumb press to be "free." It neither contributes to penalties such as "same finger" nor bonuses such as "alternation." So long as you don't put two letters on a thumb I guess...
I could expand it to include thumb keys of course, which is why I was asking for suggestions and comments.