The best practice in organising your events sheets is to keep things organised from the get go. Put things into groups logically and don't forget you can have groups within groups.
Leave yourself plenty of comments too - even for things you think are simple. Sometimes if you have to stop for whatever reason for a week or so, without good comments you are going to feel pretty lost getting back into a big project.
Forget about trying to optimise your event sheets for performance. Truly, it is not about how many events or event sheets you have - it's about what you are doing with those events. The debugger shows you where the events are that are potentially problem areas (or at least areas that you can improve performance through optimisations).
If you are creating a big game, 2 crucial things to look out for are;
1.) that you aren't overloading the gpu with too many art assets (this means building large landscapes from smaller parts that you will re-use heavily the same way all 'big' games do but you might not realise).
2.) you don't have the cpu doing unnecessary work (think of it like making sure you have turned off the light after you leave a room to save electricity). The real question is, is it possible to do this for the game you are imagining? If not you might have to make some compromise.
WackyToaster re your 1000 enemies, do these 1000 uniquely acting enemies share parts of their behavior? I have no idea what type of game you are making but that seems to me to be a bit overkill. You should try to make universal behaviors that can cover a wide range of functions/behaviors instead of creating specific ones for each whenever possible.