My character has base INT of 10. When I equip the following 2 items: helm with + 2 INT and armor with +1 INT I expect his INT to go up to 13. However this does not happen and only the helmet's bonus is applied. Is this a bug or by design?

That's by the game design. In addition, defensive stats are same. 

As the gametips repeatedly (loading screen, In Game) state that multiple bonuses to the same stat are usually not stacked, but the lesser one is supressed, I`d wager "Design".

 

A Design Decision I do not like, but well, what can you do?

This is very inconsistent, though. Some equipment bonuses DO stack, and all equipment bonuses (I think?) stack with eating food.

If you open up the Character screen and scroll down to Active Effects you can see which effects on you are being suppressed (so that you can redistribute items, for example).