It's true that we really missing some sort of "best practices" advises section with scaling an perspective topics in it. If projects start to grow, sooner or later you can hit some limits or just lose control over it if this kind of advises are not followed.
Flow based programming feels a quite bit different from what we are used to deal with (if any of course). Somehow those little things you'll need can happen too easy just by wiring known things together and by creating one easy solution next to other, the moment of that hit might be unexpected and painful.
I am creating new version of my home automation. It's just because of with first one I lost scalability. Just adding one new device turned out of 3 days of fixing. No good. But it was a great learning curve.
New version goes on complete different path. I grouped logical similarities, everyone to different flow (tab).
Something like: object creation, incoming data listeners, time based injectors, control logic, outgoing data senders, dashboard widgets (separated for every dashboard tab) and so on. So I can't lose track if something does not behave correctly because of if I can figure out the potential reason of failure, I can find the source just by failure nature. And there is no need to go wire by wire to find the source of issue.
Of course this kind of approach might be good for my project and may be for some others too but definitely not for all of them. Every project is unique. So it takes a good time of planning and experimenting before it is reasonable enough to start to make it.
But back to my point - "best practices" in this direction would be really nice.