As a Perf TSE, more volumes can be helpful. It depends on the use case. I actually would disagree as one who sees performance problems all the time, but I suppose I'm jaded. 🙂
One option is you could convert to FlexGroup using ONTAP 9.7 (new feature).
Honestly, this is worth a good chat with your account team as there are advantages and disadvantages to both.
Regarding the orignal question, in theory your dedupe time should be the same, or maybe even faster because it's multiple sets of data and ONTAP loves parallelism for getting things done faster compared to serial operations. What will likely happen is if you have a single volume that takes 2 hours, it may only take 5 minutes per volume, and add up to roughly the same total 2 hours. You could run maybe one or two jobs in parallel even, or more, depending on your available performance budget (Performance Capacity) and get it done even faster.