Why does pH decrease when diluting a base? Take a strong base such a sodium hydroxide
Adding water will result in adding a hydroxide ions as well as hydronium ions to the solution 
However if the pH decreases this means that the hydronium ion concentration will increase , hence the hydroxide ion concentration decreased 
Why is this so ? What about all the hydroxide ions that were added from the water 
I understand the mathematics behind it , but it doesn't intuitively make sense
You are overcomplicating it. The concept of pH and pOH stems from the concentration of $\ce{OH-}$ or $\ce{H+}$ per solvent unit $\ce{H2O}$, like so $\ce{\frac{[OH-]}{[H2O]}}$ or $\ce{\frac{[H+]}{[H2O]}}$. There is also a logarithm involved, but lets keep it simpler than that. You are adding far more of the denominator than the numerator, hence the fraction is becoming smaller and the pH is going towards pH of pure water.