So, there are quite a few well known metrics for this in the public health world

* Years of Life Lost (YLL) * Disability Adjusted Life Years (DALY) * Quality Adjusted Life Years (QALY)

They are calculated in an interesting way that is open for arguing and interpretation, but it provides a good baseline for the ability to compare them.

As for the double counting, this is in fact a real problem, as a lot of health problems are interlinked, and having multiple health problems have a multiplying affect on health in general.