I don't like that the players in the big clans wont get a go with the 40 player limit. And creating sub-clans isn't ideal. What it really comes down to is Kratt's question, as we could join a sub-clan for clan league, and then all hop back into the main clan for the community aspect and such.
This also raises the issue - having 3 TSFH clans and 3 TLA clans and 3 "insert clan name" etc. This would be pretty redundant if you are against your own clan buddies as a lot of clans already have their own clan leagues or just tournys every once in a while. I don't think it's fair either against some other clans, it would be pretty demoralising to see you lost to TSFH, and now you are against TSFH(2), and TSFH(3).
If you don't have a 40 player limit, then the big clans have an advantage by being able to send in more players to get more wins. This could be circumvented by ranking based on average wins per player, but it's just unnecessary and ruins the idea of getting territories for your clan (as you'd get decimals and this would just be weird and silly). So I think the 40 player limit is perfectly fine.
Also, what do you mean by sub-clan? As in one clan sends in multiple teams? Again, this is silly. Or are you thinking more of a brother/sister clan type thing? That would be fine.
Anyway, your weird sub-clan issues are all solved by a simple thing - a 40 player limit. Sure, some people will miss out, but the fact is, some people miss out! There's no way to run this that's fair or logical where everyone from a big clan can participate.