The trick is to find a filter/scrubber that will mate to your fan.
So an inline 'muffin' style blower with a 6" port will take a scrubber with a 6" opening. When you start shopping for these components it will be clearer. I'm so glad you are starting now, so you can look at the air-cooled hood if you run one, exhaust fan, and scrubber as a single unit. They are all connected, and it's most efficient if you get all the same diameter ducting for them- reducers cause turbulence, and turbulence reduces air flow.
If you are looking at a specific hood that you think is just totally the cat's ass, and it happens to be a 6" duct, your life is super easy because 6" components are REALLY REALLY common.
Also, choose your scrubber carefully. What is important? Do you need heavy duty control for a super smelly strain? Or would you compromise a bit of odor control for cheap cost and ease of disposal (=urban apartment, don't want to be seen walking down to the dumpster with a big can filter haha)? You have a choice between a rigid can filter and a fabric type like an odorsok.