Event sheets do reference other 'Included' Event sheets, but I haven't really found this an issue.
Imagine you just used one single Event sheet instead. When run, C2 would read each Event (condition -> Action) sequentially. Using multiple Event sheets is just the same thing in my head. When I include an Event sheet, I just visualize that whole block of code pasted into the main Even sheet. Because all the individual Event sheets have specific tasks, there's no overlap, but there is cross-referencing.
I do come from a programming background, so maybe that helps, as I can usually see in my head how I want something to happen, then I try to code it.
It's difficult to know what to say to you - this method works for me and many others, but it's possible that it's not for everyone.
When I first started this Manic Miner remake, I did do it all on one Event sheet, but quickly realized I was getting lost in the code. I took the decision to split the code and use Includes, which helped me greatly.
Last thought - when it boils down to it, it's best just to do whatever you are comfortable with. Maybe try a few prototyping exercises that do/do not use Includes and see what you prefer.