I understand that when you colonize too many systems your empire happyness goes bad and everyone rebels, and that the solution is either researching the +1/+2 overcolonization limit research nodes or the anti-overcolonization custom race traits. 

But how do i know how many systems i can colonize before triggering the overcolonization effect? 

My current strategy is just to colonize until i notice mass mutiny and then research the +1 node to stabilize everything. There must be a better way?

Hit F1 and watch out (somewhere on lower left side). Here you should find the current colony limit shown i.e. like this: 4/7.

When in a system with a colonization ship, the hover over will also tell you that colonizing this system will cause -10 happiness. 

But as Groo mentions, the Empire screen (F1) is the clearest way. The bar on the left panel will total your currently colonized systems / your maximum.