Did the balance changes coming to the Clown bring a ner as well?

I think what it is more specifically is a delay after reloading, as if he has to go through a cooldown to reload now instead of after he throws his bottle. I was under the assumption that they were just going to cut the cooldown/slow on Clown after he throws the bottle, but now it seems like that delay was rather just moved to happen after he reloads, which makes him feel like he loses even more distance than he should after the reload.

So yes, I indeed was experiencing what you described as "just before you're done reloading your bottles, suddenly you're 99% slowed almost to a complete halt." I guess if you do it at the right time, it still makes you lose less distance (as long as you aren't reloading after every single bottle) but as far as I'm concerned it's a bug, because they didn't say they were moving the delay to the end of his reload or anything in the patch notes.