1. Cycling isn't a weight bearing activity on your knees and hips, so tends not to wear out these joints unless the individual is predisposed. Activities like running have a much higher risk of causing arthritis. This isn't to say there are no long term health issues to cycling- 'cyclist's palsy' is a thing for example (compression and eventually damage to the ulnar nerve in the hand from leaning on handlebars). However they are fairly minor and easily compensated for on the whole (modern, proper cycling mitts/gloves have padding that lies above the hypothenar eminence on your hand, to prevent damage to the nerve). On the other hand, being overweight comes with a huge health burden:A knee replacement costs about £4000 per operation, and usually lasts for ~20years. A heart attack costs £5-6000 for the stay in hospital, and most survivors will have future heart attacks. There are also long-term medication costs to heart attacks, joint replacements usually require no ongoing therapy with a successful operation. Basically, the off-chance that someone needs a knee replacement due to their cycling is far cheaper than someone getting obese and having a heart attack, along with the many other co-morbidities that are likely to happen with obesity.An evaluation of the economic costs of chronic disease for the years 2006-2007 showed that overweight and obesity cost the NHS £5.1 billion compared to £3.3 billion for smoking.[9] The cost of people being overweight or obese to society and the economy was estimated in 2007 to be almost £16 billion.[4] The forecast of this cost increasing to almost £50 billion by 2050 prompted the 2011 Department of Health policy "A call to action on obesity in England".[10]
2. I don't really see why this stresses people so much? Unless they get stressed at lots of things, at which point a cyclist in the road is unlikely to make much difference in the overall stress situation. I drive, and I don't find myself stressed at all by cyclists, unless they do something stupid that nearly causes an accident. But then it stresses me when any road user nearly causes an accident.
3. Probably less overall than the effects of motor accidents.
Also, the latter two points are somewhat negated by more people cycling. When you reach Netherlands-levels of cycling, then 2. basically doesn't exist, and 3. is very unlikely.
In short, they are probably not counted because they probably don't have much effect overall...