This can help to clean up your hierarchies. You will see less decision panels (as different generators will work on different levels), and Structure will not need to run unnecessary checks, which are generally fast but can add-up for large structures.
It’s not only the final number of issues in a structure that is important. It's also important to check the number of issues before any filter generators are added. For example, if you add an Insert generator with several Extend generators, they may pull 100k issues into the structure, but then a Filter generator may remove most of those, so you only see a few thousand issues. Even though it looks like a small structure, it still has to add all those original issues (and then put extra effort in to remove most of them), which could result in very poor performance.
Small structures use less resources, even when you have a lot of them. It's better to create several smaller structures, custom built for specific purposes, teams or people, rather than building one big structure for everything.