What do you mean by elite? Are you talking an elite gym or just the 'elite squad' of a normal gym?
I have two DDs doing gymnastics. Both are competitive and in squads (and in the squad in their gym, competing mostly at regional level) but neither are an elite gymnast.
Dd1 is 9 and trains 18 hours a week, split over 5 days a week. She is an artistic gymnast.
DD2 is 6 and trains 7.5 hours a week; 6 hours artistic and 1.5 hours rhythmic (they / we're still deciding what route she'll go down).
From my experience I would anticipate the following issues:
Competitions - how would you manage comps if they are at different clubs? I know my gym often expects you to keep the other daughter at gym even if the one is at a comp. I'm guessing with acro, like rhythmic comps may be further afield and require overnight stays more often. How would you manage the logistics of leaving one behind whilst you went off to the comp? Or would DH be happy staying behind?
Is your son's hours going to increase? If so, by much? 12 hours is manageable, but what if it goes to 18, 20 hours etc...? Would you be able to cope then?
What are you going to do when he is at secondary school? I know my dd who is only in year 4 struggles to cope with her homework, and I dread dd2 doing different days (desperately hoping she sticks to the same days as dd1) because that would really make it difficult to complete her homework, particularly as she gets older and gets more at secondary etc.
Are the clubs close to each other, or on different days? Will they potentially train at the same times? If so, this makes it far more workable.
I don't know about acro, but I know artistic gymnastics hours increases quite dramatically. I sometimes baulk at my daughter doing 18 hours, but really that is nothing. I know one little girl who is a true elite gymnast. She trains over 25 hours a week, has to leave school early to train etc. if your daughter was an elite like this (ie at a big gym club) could you cope with that?
Finally, will this rule out playdates? I know this sounds silly, but sometimes I think this is one of the hardest things my daughters find. As they train 3 days a week after school, have an after school club one day and I work the 5th day, they don't get t do play dates very often. I know they find that hard, and that they sometimes get left out of things (parties, conversations, games etc) because they are never around after school to join in. My girls have it easier because they are friends with the girls at their gym, so we work around gym hours for play dates, but how would you cope? Would your daughter / son mind this?
If I was in your position, I would probably go for it, because I would reason that if I had given those opportunities to Dd1, I couldn't deny them to dd2. But some of the above considerations went through my mind when we were considering whether to let dd2 join the development squad for rhythmic.
Good luck with the decision, whichever way you go!