Does the Rune of the Monk’s healing bonus stack with Aquatic Benevolence

Both of the links you provide say "Stacks in duration". According to the Effect Stacking page

Effects stack in one of two ways: in intensity or in duration. For example, multiple stacks of bleeding, which stacks in intensity, increase the damage dealt over time, and multiple stacks of regeneration, which stacks in duration, increase the duration that the healing over time lasts.

It also says

The best intensity lasts for the cumulative duration

Originally I interpreted this to say higher damage trumps lesser damage but increases duration which is incorrect. Based on info I found at Guild Wars Insider the answer becomes a little more complicated.

Multiple duration effects are applied in sequence for their applicable lengths of time. In this example lets say Chilled got applied then Crippled within 10 seconds of each other and both effects are for 60 seconds in length. Chilled would get applied to you for 66% reduction, Crippled would wait until Chilled had finished then immediately get applied to you for the 50% reduction for another 60 seconds.

The blog post at Guild Wars Insider has a nice graphic to show how this stacking occurs if my explanation is confusing.

(0/2) means that you have 0 out of a possible 2 of these runes equipped. When you have 1 of these runes equipped you will get the bonus listed under (1), and when you have 2 equipped you will get the bonus listed under (2) as well.

For instance, from your screenshot you have an item that has a Minor Rune of Hoelbrak in it. If you were to equip it, you would get an extra 10 power because you now have one of this rune equipped. If you were to then equip a pair of boots with another of these runes in it you will get an extra 10% Might Duration for equipping those boots.