I'll just be short and to the point for this article.
If you only need one hidden counter, then it's fine. Use it. It saves memory. But when you need a couple or more, just use active objects.
My reasons are as follows:
#1: Less objects on the playfield: An Active Object contains three alterable values, which can do anything that a hidden counter can do. And in MMF 1.5, they have 26 of those.
#2: Less bugs due to misplacement because of similar looking icons- I'm talking about the event editor- you know, you have so many counter icons that you misplace it in the wrong column and then your game goes awry. One active object can clear all those similar icons away, especially if you change the icon.
And don't worry about space. One 1x1 active object won't add so much to the memory it takes up.
In short, when you have too many hidden counters, replace them with an active object and free up some space!