Actually, I'll put my hand up and say that I found the sunken garden to be a little underwhelming. The flowers were very pretty but since you weren't allowed to wander into the sunken part very often (ever?) you weren't always able to get the full effect.
On sunny days, having a water feature there will be a lovely addition to the flowers - I love hearing the sound of water when reading or relaxing so I'm quite happy with it. It's not as if they're taking the flowers out altogether.
I use the Horniman Gardens a lot since I don't have my own and overall they are beautiful and so long as there's still some spots for us to sit in over the summer period, it's short pain for loveliness going forward. Some of the new features are for those with kids - and to be honest, with the improvements in the Triangle, I think kids are better catered for now than they've been for years. If the Triangle work hadn't been done, then I'd be agreeing that the summer works were more disruptive to families.