There is no doubt that 'flying' as a profession is not conducive to good health. In the past some things were worse, such as aircraft pressurization, noise and 'air quality'. But previous generations of pilots had the luxury of working less hours.
Nowadays, the biggest issues wrt to our health....... is Flight Time Limitations. Not only are these rules interpreted differently by each and every airline, the governing authorities are not up to the task of ensuring that pilots are probably rested. The immediate concern is obviously flight safety which obviously is not a 'true' consideration for many airline managers. So why should we expect that the second big concern.... ''pilot long term health'''..... should even enter into their little minds?
Going to the gym or going for a run on layovers if your best option. But since we are working so much more, fewer pilots are inclined to make that effort.