There are a couple of things you can do to handle very large zones. First you can try to break them in multiple zones, even if all the recipes/datasets should really be part of a single zone. You can break them in many different ways, I tend to prefer use to use alphabet like this (for groups of 5 letters): A-E, F-J, K-O, P-T and U-Z. That way you know which zone to look for if you know the first dataset letter. If you don't want to break on multiple zones you still can use some tricks to experience a better GUI. You can collapse large zones (right click over the zone, Collapse) which make viewing the rest of the flow difficult. You can also "maximise" a single zone (right click, Open) to focus your attention on a single zone.
Finally Zones can be managed via the Python API if you need to make bulk changes to many datasets:
https://developer.dataiku.com/latest/concepts-and-examples/flow.html#creating-a-zone-and-adding-item...
